Software Updates

Simulaid

a collection of utilities designed to help setting up and analyze molecular simulations.

Gamma

(General Approach to Magnetic resonance Mathematical Analysis) a package of C++ libraries that allow simulation of magnetic resonance (NMR, MRS) experiments. It is used for designing and analyzing NMR pulse sequences.

USF Gerard Utilities

a Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.

And includes the following binaries:

• aconio
• cello
• comap
• crave
• essens
• flood
• lsqman
• mama.debug
• mapman
• mave
• moleman2
• o2d
• oops
• prof
• site2rt
• solex
• ssencs
• xpand

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

FREALIGN

(Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

FREALIGN

(Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.

PyMOL

a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

FREALIGN

(Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.

REFMAC

a program that carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. It also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where missing data have been restored.

O

a model building application for X-ray crystallography.

PyMOL

a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

iMosflm

a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package.

REFMAC

a program that carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. It also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where missing data have been restored.

O

a model building application for X-ray crystallography.

CNS

(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

REFMAC

a program that carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. It also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where missing data have been restored.

AUTO3DEM

an automated image reconstruction system that coordinates the execution of the parallel, numerically-intensive codes P3DR, PCUT, POR, PPFT, PSF and RobEM (a GUI driven program used both for image preprocessing and visualization).

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

Reduce

a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.

FASTA

a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.

AUTO3DEM

an automated image reconstruction system that coordinates the execution of the parallel, numerically-intensive codes P3DR, PCUT, POR, PPFT, PSF and RobEM (a GUI driven program used both for image preprocessing and visualization).

CTF

a group of programs for finding CTFs of electron micrographs; CTFFIND3 and CTFTILT.

REFMAC

a program that carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. It also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where missing data have been restored.

O

a model building application for X-ray crystallography.

Reduce

a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.

FASTA

a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.

CTF

a group of programs for finding CTFs of electron micrographs; CTFFIND3 and CTFTILT.

O

a model building application for X-ray crystallography.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

CNS

(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement.

DSSP

a program that standardizes secondary structure assignment calculated from a coordinate file. Secondary structure prediction is not supported. Designed by Wolfgang Kabsch and Chris Sander

CTF

a group of programs for finding CTFs of electron micrographs; CTFFIND3 and CTFTILT.

FASTA

a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.

APBS

(Adaptive Poisson-Boltzmann Solver) a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE), solves the equations of continuum electrostatics for large biomolecular assemblages.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

AUTO3DEM

an automated image reconstruction system that coordinates the execution of the parallel, numerically-intensive codes P3DR, PCUT, POR, PPFT, PSF and RobEM (a GUI driven program used both for image preprocessing and visualization).

MGLTools

a software package for visualization and analysis of molecular structures comprising AutoDockTools (ADT): a graphical front-end for setting up and running AutoDock; Python Molecule Viewer (PMV); and Vision: a visual-programming environment for building networks describing novel combinations of computational methods and yielding new visualizations of their data.

VMD

a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

MOSFLM

a package for processing film and image plate data.

APBS

(Adaptive Poisson-Boltzmann Solver) a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE), solves the equations of continuum electrostatics for large biomolecular assemblages.

Reduce

a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.

O

a model building application for X-ray crystallography.

EMBOSS

a program that integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

DSSP

a program that standardizes secondary structure assignment calculated from a coordinate file. Secondary structure prediction is not supported. Designed by Wolfgang Kabsch and Chris Sander

2dx

a package (consisting of a suite of five programs: 2dx_manager, 2dx_image, 2dx_diffraction, 2dx_merger and 2dx_logbrowser) for user-friendly image processing of 2D crystals.

PFT3dr

a tool that performs orientation searches and positional refinement of icosahedral viruses.

MOSFLM

a package for processing film and image plate data.

VMD

a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

EPMR

a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes three rotational and three positional parameters for the search model with respect to the correlation coefficient between Fo and Fc.

Theseus

a program for the simultaneous superpositioning and analysis of multiple macromolecular structures via the method of maximum likelihood (ML).

MGLTools

a software package for visualization and analysis of molecular structures comprising AutoDockTools (ADT): a graphical front-end for setting up and running AutoDock; Python Molecule Viewer (PMV); and Vision: a visual-programming environment for building networks describing novel combinations of computational methods and yielding new visualizations of their data.

BLAST

(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

EMBOSS

a program that integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

CNS

(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement.

FASTA

a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.

Reduce

a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.

CARA

(Computer Aided Resonance Assignment) an application for the analysis of NMR spectra and computer-aided resonance assignment.

relax

a software package designed for the study of molecular dynamics by NMR data analysis.

Gnuplot

a portable command-line driven graphing utility originally created to allow scientists and students to visualize mathematical functions and data interactively. It has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like CCP4 and Octave.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

Theseus

a program for the simultaneous superpositioning and analysis of multiple macromolecular structures via the method of maximum likelihood (ML).

SOLVE/RESOLVE

a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.

O

a model building application for X-ray crystallography.

BLAST

(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

DSSP

a program that standardizes secondary structure assignment calculated from a coordinate file. Secondary structure prediction is not supported. Designed by Wolfgang Kabsch and Chris Sander

Raster3D

a set of tools for generating high quality raster images of proteins or other molecules.

CTF

a group of programs for finding CTFs of electron micrographs; CTFFIND3 and CTFTILT.

R

a free software environment for statistical computing and graphics.

relax

a software package designed for the study of molecular dynamics by NMR data analysis.

EPMR

a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes three rotational and three positional parameters for the search model with respect to the correlation coefficient between Fo and Fc.

ImageJ

a Java image processing program inspired by NIH Image that can display, edit, analyze, process, save and print 8-bit, 16-bit, and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw" and supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.

O

a model building application for X-ray crystallography.

SHELX-97

a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately.

ProFit

a program for the ultimate protein least squares fitting.

PFT3dr

a tool that performs orientation searches and positional refinement of icosahedral viruses.

R

a free software environment for statistical computing and graphics.

APBS

(Adaptive Poisson-Boltzmann Solver) a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE), solves the equations of continuum electrostatics for large biomolecular assemblages.

NMRVIEW

a tool used to visualize and Analyze Nuclear Magnetic Resonance Data.

SOLVE/RESOLVE

a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.

EMBOSS

a program that integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

relax

a software package designed for the study of molecular dynamics by NMR data analysis.

Rasmol

a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

AUTO3DEM

an automated image reconstruction system that coordinates the execution of the parallel, numerically-intensive codes P3DR, PCUT, POR, PPFT, PSF and RobEM (a GUI driven program used both for image preprocessing and visualization).

Reduce

a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

HKL2MAP

a graphical user-interface for macromolecular phasing.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

CARA

(Computer Aided Resonance Assignment) an application for the analysis of NMR spectra and computer-aided resonance assignment.

NMRVIEW

a tool used to visualize and Analyze Nuclear Magnetic Resonance Data.

DINO

a realtime 3D visualization program for structural biology data.

Theseus

a program for the simultaneous superpositioning and analysis of multiple macromolecular structures via the method of maximum likelihood (ML).

Xmipp

(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

DSSR

(Dissecting the Spatial Structure of RNA) a software tool for dissecting the spatial structure of RNA.

d*TREK

a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

OpenBabel

a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

2dx

a package (consisting of a suite of five programs: 2dx_manager, 2dx_image, 2dx_diffraction, 2dx_merger and 2dx_logbrowser) for user-friendly image processing of 2D crystals.

relax

a software package designed for the study of molecular dynamics by NMR data analysis.

Graphviz

an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php

CNS

(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement.

AutoDock

a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of a known 3D structure.

Raster3D

a set of tools for generating high quality raster images of proteins or other molecules.

Rasmol

a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

Clustal

a general purpose multiple sequence alignment program for DNA or proteins.

CS-ROSETTA

(Chemical-Shift-ROSETTA) a robust protocol to exploit mining of protein chemical shifts deposited in the BMRB, in conjunction with the known corresponding 3D structures for de novo protein structure generation, using as input parameters the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts. Also includes CS-Rosetta toolbox, which provides useful scripts for preparing, running, and analyzing CS-Rosetta runs.

R

a free software environment for statistical computing and graphics.

AutoDock

a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of a known 3D structure.

HKL2MAP

a graphical user-interface for macromolecular phasing.

MGLTools

a software package for visualization and analysis of molecular structures comprising AutoDockTools (ADT): a graphical front-end for setting up and running AutoDock; Python Molecule Viewer (PMV); and Vision: a visual-programming environment for building networks describing novel combinations of computational methods and yielding new visualizations of their data.

Theseus

a program for the simultaneous superpositioning and analysis of multiple macromolecular structures via the method of maximum likelihood (ML).

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

ALBULA

a fast and easy-to-use program that allows optimal visualization of PILATUS and EIGER data, and ALBULA API, a Python programming interface for displaying images and performing operations and calculations. The API enables you to easily integrate the viewer functionality into your beamline infrastructure or experimental setup. Consists of the standalone program ALBULA VIEWER.

DINO

a realtime 3D visualization program for structural biology data.

LAFIRE

(Local-correlation-coefficient-based Automatic FItting for REfinement) an automatic refinement system for protein crystallography. The system starts with an initial model (approximate or partial model) and finishes with the final structure including water molecules. LAFIRE uses the refinement programs CNS or Refmac5.

Probe

an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.

Sparky

a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.

PHYLIP

a free package of software programs for inferring phylogenies.

SHELX-97

a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately.

HADDOCK

(High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions.

Xmipp

(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.

NMRVIEW

a tool used to visualize and Analyze Nuclear Magnetic Resonance Data.

Graphviz

an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php

CS-ROSETTA

(Chemical-Shift-ROSETTA) a robust protocol to exploit mining of protein chemical shifts deposited in the BMRB, in conjunction with the known corresponding 3D structures for de novo protein structure generation, using as input parameters the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts. Also includes CS-Rosetta toolbox, which provides useful scripts for preparing, running, and analyzing CS-Rosetta runs.

OpenBabel

a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

d*TREK

a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

R

a free software environment for statistical computing and graphics.

em2em

a program to convert images from/to formats used in the "electron microscopical community" (3DEM)

MAMMOTH-Mult

a package that does multiple alignment of protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.

NUCPLOT

a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded protein-DNA, DNA-ligand and protein-RNA complexes.

ProFit

a program for the ultimate protein least squares fitting.

BLAST

(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

Probe

an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.

PHYLIP

a free package of software programs for inferring phylogenies.

HADDOCK

(High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions.

PFT3dr

a tool that performs orientation searches and positional refinement of icosahedral viruses.

R

a free software environment for statistical computing and graphics.

MOLE

a universal toolkit rapid, automated location and characterization of channels and pores in molecular structures. The core of the MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. It can explore large molecular channels, complex networks of channels, and molecular dynamics trajectories that requires analysis of a large number of snapshots.

Primer3

a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.

Spire

a graphical user interface for executing SPIDER batch files and other programs, Spire offers a way to manage and organize the many output files created by SPIDER during reconstruction projects.

ALBULA

a fast and easy-to-use program that allows optimal visualization of PILATUS and EIGER data, and ALBULA API, a Python programming interface for displaying images and performing operations and calculations. The API enables you to easily integrate the viewer functionality into your beamline infrastructure or experimental setup. Consists of the standalone program ALBULA VIEWER.

ULTRASCAN2

a software package for comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments.

CTFFIND 4

a new version of ctffind (a program for finding CTFs of electron micrographs) that should run significantly faster than CTFFIND 3 and may give slightly improved results when processing data from detectors other than scanned photographic film.

DOCK

a molecular docking application used to a) predict binding modes of small molecule-protein complexes; b) search databases of ligands for compounds that inhibit enzyme activity, bind a particular protein, bind nucleic acid targets; c) examine possible binding orientations of protein-protein and protein-DNA complexes; d) help guide synthetic efforts by examining small molecules that are computationally derivatized. Dock is offered in the SBGrid collection in two iterations, Dock 3 and Dock 6.

Ringer

a program to detect molecular motions by automatic electron density sampling.

CONCOORD

a method to generate protein conformations around a known structure based on geometric restrictions.

Primer3

a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.

NUCCYL

a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.

PROCHECK

a program for checking the stereochemical quality of a protein structure, producing a number of PostScript plots analyzing its overall and residue-by-residue geometry.

R

a free software environment for statistical computing and graphics.

Elves

a tool that automates most of the repetitive and mindless procedures used in solving macromolecular crystal structures, and is capable of autonomously carrying out all the steps needed to convert raw X-ray diffraction image data to a phased electron density map.

PHYLIP

a free package of software programs for inferring phylogenies.

EMBOSS

a program that integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

Graphviz

an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php

EMAN

a suite of scientific image processing tools with a particular focus on single particle reconstruction and which includes Foldhunter and Helixhunter.

PFT3dr

a tool that performs orientation searches and positional refinement of icosahedral viruses.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

MUSCLE

(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.

Raster3D

a set of tools for generating high quality raster images of proteins or other molecules.

Clustal

a general purpose multiple sequence alignment program for DNA or proteins.

DelPhi

a program for calculating protein electrostatics.

Rasmol

a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

Maxit

an application that assists in the processing and curation of macromolecular structure data.

HKL2MAP

a graphical user-interface for macromolecular phasing.

AutoDock

a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of a known 3D structure.

AMIGOS II

a tool that allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.

SOLVE/RESOLVE

a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.

BALBES

a system that aims to integrate into one system all the components necessary for finding a solution structure by MR. It consists of a database, scientific programs and a python pipeline. The system is automated and needs no user intervention when running a complicated combination of jobs, such as model searching, molecular replacement and refinement.

HADDOCK

(High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions.

ULTRASCAN2

a software package for comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments.

Probe

an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.

LAFIRE

(Local-correlation-coefficient-based Automatic FItting for REfinement) an automatic refinement system for protein crystallography. The system starts with an initial model (approximate or partial model) and finishes with the final structure including water molecules. LAFIRE uses the refinement programs CNS or Refmac5.

STAMP

(STructural Alignment of Multiple Proteins) a suite of programs to compare and align protein 3-D structures. It will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. It will also search a database of protein structures to identify structurally similar proteins and includes a number of utility programs for the manipulation of protein structures.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

PyTOM

a tool that unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.

Protomo

a system that includes programs and shell scripts for electron tomography of thin specimens, providing an interactive graphical tool for fast initial alignment of a tilt series, shell scripts for the more time consuming refinement, and some other useful image manipulation utilities.

WHAT_CHECK

a protein verification tool from the WHAT IF program available as a free stand-alone program, complete with all source code.

Gorgon

an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.

ProtSkin

a tool that converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP program or the MOLMOL program or the PyMOL program. A pseudo-PDB file with the sequence conservation score in place of the temperature factor is also provided, to use with programs such as InsightII (accelrys).

PHYLIP

a free package of software programs for inferring phylogenies.

ESPript

(Easy Sequencing in Postscript) a utility to generate a pretty PostScript output from aligned sequences and coordinate files.

istHMS

an algorithm to reconstruct non-uniformly acquired NMR data.

ALBULA

a fast and easy-to-use program that allows optimal visualization of PILATUS and EIGER data, and ALBULA API, a Python programming interface for displaying images and performing operations and calculations. The API enables you to easily integrate the viewer functionality into your beamline infrastructure or experimental setup. Consists of the standalone program ALBULA VIEWER.

diffmap

a program to calculate difference maps between two density maps. The maps must have the same overall dimensions and need to be aligned with each other.

crop

a program for cutting sections out of 2D and 3D density maps.

AMIGOS II

a tool that allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.

SHELX-97

a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately.

QUILT

a program that detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.

d*TREK

a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

DynDom

a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.

EMAN

a suite of scientific image processing tools with a particular focus on single particle reconstruction and which includes Foldhunter and Helixhunter.

Sparky

a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.

PDB2PQR

a Python package that automates structure preparation tasks for continuum electrostatics calculations. It can convert protein files in PDB format to PQR format. It can add a limited number of missing heavy atoms to biomolecular structures, determine side-chain pKas, placing missing hydrogens, optimize the protein for favorable hydrogen bonding, and assign charge and radius parameters from a variety of force fields.

SOLVE/RESOLVE

a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

DelPhi

a program for calculating protein electrostatics.

O

a model building application for X-ray crystallography.

EM-BFACTOR

a program that allows sharpening of high resolution information in 3D maps obtained by electron cryomicroscopy according to the Rosenthal and Henderson approach (JMB 333:721-745, 2003).

ProFit

a program for the ultimate protein least squares fitting.

MAMMOTH-Mult

a package that does multiple alignment of protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.

Maxit

an application that assists in the processing and curation of macromolecular structure data.

FinchTV

a popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multi-pane view. And it leads the way with raw data views, BLAST searching and the ability to reverse complement sequences and traces.

CONCOORD

a method to generate protein conformations around a known structure based on geometric restrictions.

Remediator

a tool that converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2).

Raster3D

a set of tools for generating high quality raster images of proteins or other molecules.

NMRVIEW

a tool used to visualize and Analyze Nuclear Magnetic Resonance Data.

Rasmol

a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

NUCPLOT

a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded protein-DNA, DNA-ligand and protein-RNA complexes.

Fiji

an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

NUCCYL

a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.

MOLE

a universal toolkit rapid, automated location and characterization of channels and pores in molecular structures. The core of the MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. It can explore large molecular channels, complex networks of channels, and molecular dynamics trajectories that requires analysis of a large number of snapshots.

Avogadro

an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

SSAHA2

(Sequence Search and Alignment by Hashing Algorithm) a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.

SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.

bfactor

a program for filtering 3D maps and applying B-factors.

BALBES

a system that aims to integrate into one system all the components necessary for finding a solution structure by MR. It consists of a database, scientific programs and a python pipeline. The system is automated and needs no user intervention when running a complicated combination of jobs, such as model searching, molecular replacement and refinement.

R

a free software environment for statistical computing and graphics.

Ghostscript

an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.

PyTOM

a tool that unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

CONCOORD

a method to generate protein conformations around a known structure based on geometric restrictions.

Probe

an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.

Spring

(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.

breseq

a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.

BEST

a program for optimal planning of X-ray data collection from protein crystals.

istHMS

an algorithm to reconstruct non-uniformly acquired NMR data.

SnB

a computer program for the determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites. Based on Shake-and-Bake (a dual-space direct-methods procedure).

Remediator

a tool that converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2).

DireX

a tool that performs efficient geometry-based conformational sampling of protein structures under experimental restraints. It combines prior structural information with experimental data through the Deformable Elastic Network (DEN) approach which drastically reduces over-fitting.

NUCPLOT

a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded protein-DNA, DNA-ligand and protein-RNA complexes.

EM-BFACTOR

a program that allows sharpening of high resolution information in 3D maps obtained by electron cryomicroscopy according to the Rosenthal and Henderson approach (JMB 333:721-745, 2003).

Surface Racer

a program that calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside.

diffmap

a program to calculate difference maps between two density maps. The maps must have the same overall dimensions and need to be aligned with each other.

SSAHA2

(Sequence Search and Alignment by Hashing Algorithm) a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.

SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.

SAM

(Sequence Alignment and Modeling system) a collection of tools for creating, refining, and using linear hidden Markov models for biological sequence analysis.

O

a model building application for X-ray crystallography.

IPLT

(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk.

crop

a program for cutting sections out of 2D and 3D density maps.

Fiji

an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

T-Coffee

a multiple sequence alignment package that can be used to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).

bfactor

a program for filtering 3D maps and applying B-factors.

NUCCYL

a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.

ESPript

(Easy Sequencing in Postscript) a utility to generate a pretty PostScript output from aligned sequences and coordinate files.

CMView

an interactive contact map visualization and analysis tool.

QUILT

a program that detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.

d*TREK

a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

POVRAY

(Persistence of Vision Raytracer) a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Windows, Mac OS/Mac OS X and i86 Linux. The source code is available for those wanting to do their own ports. POVRAY was originally written by David Kirk Buck and Aaron A. Collins.

SIGNATURE

an automated particle selection system for electron microscopy. The application was written by James Chen in Niko Grigorieff laboratory at Brandeis.

ProtSkin

a tool that converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP program or the MOLMOL program or the PyMOL program. A pseudo-PDB file with the sequence conservation score in place of the temperature factor is also provided, to use with programs such as InsightII (accelrys).

R

a free software environment for statistical computing and graphics.

DynDom

a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.

DelPhi

a program for calculating protein electrostatics.

Avogadro

an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

Protomo

a system that includes programs and shell scripts for electron tomography of thin specimens, providing an interactive graphical tool for fast initial alignment of a tilt series, shell scripts for the more time consuming refinement, and some other useful image manipulation utilities.

PDB2PQR

a Python package that automates structure preparation tasks for continuum electrostatics calculations. It can convert protein files in PDB format to PQR format. It can add a limited number of missing heavy atoms to biomolecular structures, determine side-chain pKas, placing missing hydrogens, optimize the protein for favorable hydrogen bonding, and assign charge and radius parameters from a variety of force fields.

Elves

a tool that automates most of the repetitive and mindless procedures used in solving macromolecular crystal structures, and is capable of autonomously carrying out all the steps needed to convert raw X-ray diffraction image data to a phased electron density map.

Nessy

an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY autamatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models.

MUSCLE

(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.

DPS

(Data Processing Suite) a suite of programs for processing single crystal X-ray diffraction data of proteins, viruses, nucleic acids and other large biological complexes, with an emphasis on data collected at synchrotron sources.

PROCHECK

a program for checking the stereochemical quality of a protein structure, producing a number of PostScript plots analyzing its overall and residue-by-residue geometry.

CCP4mg

a tool that offers a quick and easy way to create beautiful publication quality images and movies and to superpose and analyze structures.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

SamViewer

a 2D image display and analysis program, specifically designed for single-particle EM.

Gamma

(General Approach to Magnetic resonance Mathematical Analysis) a package of C++ libraries that allow simulation of magnetic resonance (NMR, MRS) experiments. It is used for designing and analyzing NMR pulse sequences.

Pysam

a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API; it provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages.

Pysam is installed as a module within python.

Toronto Single Particle Cryo-EM Software Tool Collection

a collection of software tools for computational analysis of cryo-EM images developed by John Rubinstein/U Toronto

STAMP

(STructural Alignment of Multiple Proteins) a suite of programs to compare and align protein 3-D structures. It will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. It will also search a database of protein structures to identify structurally similar proteins and includes a number of utility programs for the manipulation of protein structures.

pandas

a library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.

pandas is installed as a module within python.

Spring

(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.

ProtSkin

a tool that converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP program or the MOLMOL program or the PyMOL program. A pseudo-PDB file with the sequence conservation score in place of the temperature factor is also provided, to use with programs such as InsightII (accelrys).

MAIN

a model building application for X-ray crystallography.

ProFit

a program for the ultimate protein least squares fitting.

VMD

a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

WebLogo

a set of command line tools for sequence logo generation.

CONCOORD

a method to generate protein conformations around a known structure based on geometric restrictions.

T-Coffee

a multiple sequence alignment package that can be used to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).

d*TREK

a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

AMPS

(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.

PDB2PQR

a Python package that automates structure preparation tasks for continuum electrostatics calculations. It can convert protein files in PDB format to PQR format. It can add a limited number of missing heavy atoms to biomolecular structures, determine side-chain pKas, placing missing hydrogens, optimize the protein for favorable hydrogen bonding, and assign charge and radius parameters from a variety of force fields.

PDB_REDO

a program that refines any structural model you are working on, by optimising REFMAC refinement and by partial model rebuilding. The process is fully automated so you only need to provide an initial structure model and your reflection data.

bfactor

a program for filtering 3D maps and applying B-factors.

istHMS

an algorithm to reconstruct non-uniformly acquired NMR data.

Avogadro

an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

SnB

a computer program for the determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites. Based on Shake-and-Bake (a dual-space direct-methods procedure).

MAMMOTH-Mult

a package that does multiple alignment of protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.

LAFIRE

(Local-correlation-coefficient-based Automatic FItting for REfinement) an automatic refinement system for protein crystallography. The system starts with an initial model (approximate or partial model) and finishes with the final structure including water molecules. LAFIRE uses the refinement programs CNS or Refmac5.

Mead

a program that is used for including solvation effects in biological systems, such as proteins, using an atomic model of the protein. This is done by solving the Poisson-Boltzmann equation in a dielectric medium, including distributed point charges on a grid.

Spire

a graphical user interface for executing SPIDER batch files and other programs, Spire offers a way to manage and organize the many output files created by SPIDER during reconstruction projects.

SamViewer

a 2D image display and analysis program, specifically designed for single-particle EM.

Maxit

an application that assists in the processing and curation of macromolecular structure data.

Rasmol

a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

DireX

a tool that performs efficient geometry-based conformational sampling of protein structures under experimental restraints. It combines prior structural information with experimental data through the Deformable Elastic Network (DEN) approach which drastically reduces over-fitting.

SSAHA2

(Sequence Search and Alignment by Hashing Algorithm) a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.

SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.

STAMP

(STructural Alignment of Multiple Proteins) a suite of programs to compare and align protein 3-D structures. It will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. It will also search a database of protein structures to identify structurally similar proteins and includes a number of utility programs for the manipulation of protein structures.

MOLE

a universal toolkit rapid, automated location and characterization of channels and pores in molecular structures. The core of the MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. It can explore large molecular channels, complex networks of channels, and molecular dynamics trajectories that requires analysis of a large number of snapshots.

DynDom

a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.

SAM

(Sequence Alignment and Modeling system) a collection of tools for creating, refining, and using linear hidden Markov models for biological sequence analysis.

NUCCYL

a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.

NUCPLOT

a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded protein-DNA, DNA-ligand and protein-RNA complexes.

FRODOCK

(Fast Rotational DOCKing) a tool used to efficiently generate many potential predictions of how two proteins could interact.

Graphviz

an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php

RStudio

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

ALBULA

a fast and easy-to-use program that allows optimal visualization of PILATUS and EIGER data, and ALBULA API, a Python programming interface for displaying images and performing operations and calculations. The API enables you to easily integrate the viewer functionality into your beamline infrastructure or experimental setup. Consists of the standalone program ALBULA VIEWER.

MOLMOL

a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules.

O

a model building application for X-ray crystallography.

MRC Cambridge Image Processing System

a system that determines the structure of macromolecular assemblies. The approach has been to study specimens with some form of symmetry, such as crystals or helical and icosahedral particles, using programs suitable for many kinds of 2-D and 3-D analysis.

Sparky

a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.

CPMGFit

a program for non-linear least squares fitting of CPMG relaxation dispersion curves.

ModelFree

a program to fit the extended model free spectral density function to NMR spin relaxation data. The program can analyze the spin-lattice relaxation rate constant (R1), the spin-spin relaxation rate constant (R2), and the heteronuclear steady-state {1H}-X nuclear Overhauser effect (NOE) for any combination of 13C and 15N spins at up to five static magnetic fields.

PROCHECK

a program for checking the stereochemical quality of a protein structure, producing a number of PostScript plots analyzing its overall and residue-by-residue geometry.

QUILT

a program that detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.

Ringer

a program to detect molecular motions by automatic electron density sampling.

Swiss-PdbViewer

an application that provides a user friendly interface allowing you to analyze several proteins at the same time.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

Remediator

a tool that converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2).

SHELX-97

a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately.

BnP

(Buffalo n' Pittsburgh Interface) a program that combines SnB and the Phases Suite; for complete protein phasing.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

pandas

a library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.

pandas is installed as a module within python.

Pysam

a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API; it provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages.

Pysam is installed as a module within python.

Grace

a general plotting, curve fitting and data transformation program.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Staden

a set of DNA sequence assembly, editing and analyzing tools developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

Toronto Single Particle Cryo-EM Software Tool Collection

a collection of software tools for computational analysis of cryo-EM images developed by John Rubinstein/U Toronto

SpecView

a tool that provides a fast way to visualize NMR spectrum and peak data. It supports 2D and 3D graphical display modes for multidimensional and simple 1D spectra. Can automatically import spectra and peaks from many different file formats without user intervention. Spectra may be frequency referenced and superposed within the program.

CCP4mg

a tool that offers a quick and easy way to create beautiful publication quality images and movies and to superpose and analyze structures.

Nessy

an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY autamatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models.

SIMPLE

(Single-particle IMage Processing Linux Engine) does ab initio 3D reconstruction (programs cluster & origami), heterogeneity analysis (programs cluster, origami & cycler), and high-resolution refinement (programs align, reconstruct, automask & cycler).

Ruby

a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.

d*TREK (Free)

a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors. This entry is for the free version of d*TREK.

PALES

(Prediction of ALignmEnt from Structure) a software for the analysis of residual dipolar couplings and for the prediction of the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein/nucleic acid/oligosaccharide) three-dimensional shape.

Python Macromolecular Library

a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.

CPMGFit

a program for non-linear least squares fitting of CPMG relaxation dispersion curves.

MCCE

(Multi-Conformation Continuum Electrostatics) a biophysics simulation program combining continuum electrostatics and molecular mechanics. In this program, the protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics.

iMODFit

an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates.

Dowser

a program that surveys a protein molecule's structure to locate internal cavities and assess hydrophilicity in terms of the energy of interaction of a water molecule with the surrounding atoms. Experience has shown that cavities with interaction energies below -12 kcal/mol tend to be filled, and cavities for which the energy is above that threshold, tend to be empty.

DynDom3D

a program to analyze domain movements in large, multi-chain, biomolecular complexes, useful for any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement.

ESCET

a script driven program that analyzes and compares three-dimensional protein structures. The current version (0.7) is mostly designed to find the rigid part of protein molecules by comparing different structures.

TkDiff

a graphical front end to the diff program. It provides a side-by-side view of the differences between two files, along with several innovative features such as diff bookmarks and a graphical map of differences for quick navigation.

MAIN

a model building application for X-ray crystallography.

Electra

(ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography.

POVRAY

(Persistence of Vision Raytracer) a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Windows, Mac OS/Mac OS X and i86 Linux. The source code is available for those wanting to do their own ports. POVRAY was originally written by David Kirk Buck and Aaron A. Collins.

Probe

an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.

BOBSCRIPT

an extension to Molscript that adds sticks and spheres, stereo pictures, flexible colouring (colour ramping) and map drawing.

HBPLUS

a program suite (hbplus, access and clean) to compute hydrogen positions, hydrogen bonds, and neighboring interactions. The application was developed at University College London.

EM-BFACTOR

a program that allows sharpening of high resolution information in 3D maps obtained by electron cryomicroscopy according to the Rosenthal and Henderson approach (JMB 333:721-745, 2003).

NETBLAST

a simple command-line program that allows you to submit a single file of FASTA sequences over an internet connection to the NCBI BLAST databases. Searches are submitted through the client to the NCBI servers and do not need to download the databases locally (also called netblast and blastcl3).

WHAT_CHECK

a protein verification tool from the WHAT IF program available as a free stand-alone program, complete with all source code.

PHASES

a program that computes phase angles for diffraction data from macromolecular crystals with programs for merging and scaling of native and derivative data sets; analyzing difference statistics; computing Patterson and electron density maps; searching for peaks; refining heavy atoms (or protein domains as rigid groups); computing phases by MIR, SIR, SAS, SIRAS, MIRAS, or from atomic coordinates for an input model; noncrystallographic symmetry averaging; combining phases from a partial structure with MIR etc phases; computation and analysis of cross difference or Bijvoet difference Fourier maps; and for phase extension and refinement.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

ProtSkin

a tool that converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP program or the MOLMOL program or the PyMOL program. A pseudo-PDB file with the sequence conservation score in place of the temperature factor is also provided, to use with programs such as InsightII (accelrys).

Remediator

a tool that converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2).

Ringer

a program to detect molecular motions by automatic electron density sampling.

fpocket

an open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program.

XDS-Viewer

an X-ray diffraction and control image viewing utility for data processed using the XDS program package.

Protomo

a system that includes programs and shell scripts for electron tomography of thin specimens, providing an interactive graphical tool for fast initial alignment of a tilt series, shell scripts for the more time consuming refinement, and some other useful image manipulation utilities.

PGPLOT

a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs.

Unblur

a tool used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format and generates frame sums that can be used in subsequent image processing.

RASPnmr

(Protein NMR backbone resonance assignment) a tool that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy to enable rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins.

R

a free software environment for statistical computing and graphics.

PDB2PQR

a Python package that automates structure preparation tasks for continuum electrostatics calculations. It can convert protein files in PDB format to PQR format. It can add a limited number of missing heavy atoms to biomolecular structures, determine side-chain pKas, placing missing hydrogens, optimize the protein for favorable hydrogen bonding, and assign charge and radius parameters from a variety of force fields.

SCC

a suite of programs for sequence alignment: 1) aln: Pairwise alignment of biological sequences supporting spliced alignment procedures; 2) swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm; 3) prrn: global multiple alignment of a set of protein or DNA sequences by doubly-nested iterative refinement method; 4) phyln: UPGMA or NJ method to make a phylogenetic tree from a multiple alignment. 5) makmdm: constructs binary PAM matrices.

MMTSB Toolset

(Multiscale Modeling Tools for Structural Biology) a collection of perl-based user-level utilities as well as programming libraries for multiscale protein structure modeling. Intended applications include protein structure prediction, loop modeling, structure refinement, and structure evaluation/scoring.

SHELX-97

a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately.

REDCAT

a residual dipolar coupling analysis tool.

For-profit users interested in using this tool should contact Homayoun Valafar at hvalafar@gmail.com to inquire.

RMERGE

a tool. that calculates Rpim for merging, which HKL (scalepack) does not. There's no official manual right now but you can see Cell 147, 199-208 for more information.

Matt

a multiple protein structure alignment program. It uses local geometry to align segments of two sets of proteins, allowing limited bends in the backbones between the segments.

Elves

a tool that automates most of the repetitive and mindless procedures used in solving macromolecular crystal structures, and is capable of autonomously carrying out all the steps needed to convert raw X-ray diffraction image data to a phased electron density map.

SHIFTX2

a program that predicts the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input.

Curves+

a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr.

MolScript

a program for creating schematic or detailed, publication-quality molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures.

iMOD (NMA)

a toolkit to perform Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic structures. Vibrational analysis, motion animations, morphing trajectories and Monte-Carlo simulations can be easily carried out at different scales of resolution using this toolkit.

Zephyr

a tool for analyzing and manipulating images, especially those generated for electron microscopy. Zephyr is scriptable in Python, easy to extend, and easy to link to other programs.

Solvate

a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations.

RNAView

a tool that quickly displays the secondary structure of RNA/DNA with tertiary interactions. It is fully implemented with Leontis and Westhof's ( RNA (2001) 7, 499-512), convention for the edge-to-edge hydrogen bonding interactions.

IPLT

(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk.

mrtailor

a PDB preparation tool for use with ProSmart or for Molecular Replacement

NEdit

a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with thorough functionality and stability.

EMIP

(EM Imaging Processing GUI) a Graphical User Interface that collects information from the user and runs existing programs from a variety of different software packages.

FAST ModelFree

a Perl program to assist in the analysis of laboratory frame spin relaxation data. It interfaces with ModelFree 4.01 (A. G. Palmer, Columbia University) and fully automates the process of model selection and tensor optimization.

PHOELIX

a software package for image processing of helical macromolecular complexes.

Spring

(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.

CNS

(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement.

ResMap

(Resolution Map) a Python (NumPy/SciPy) application with a Tkinter GUI. It is an easy to use software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM). ResMap has a both a GUI (window) and a command line interface.

PROBCONS

an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Tigris

an open source suite of classes and programs implemented in C++ for single particle electron microscopic image processing.

Suprim

a flexible, modular software package intended primarily for the processing of transmission electron micrographs. One of several applications developed by Automated Molecular Imaging Group at The Scripps Research Institute.

Tiltpicker

a graphical user interface for picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR). TiltPicker borrows its interface from Leginon and re-implements many of the tilt picking features of SPIDER WEB that can be run on modern computers.

PROMALS

(PROfile Multiple Alignment with predicted Local Structure) a progressive method for aligning multiple protein sequences, with enhanced profile information from database searches and secondary structure prediction.

MotionCorr

a program that corrects whole frame image motion recorded with dose fractionated image stacks.

PARTICLE

a software package for single-particle EM image processing. It provides an integrated computing environment with comprehensive data analysis functions for particle selection, particle classification, 3D reconstruction and model evaluation. In addition, PARTICLE emphasizes on data visualization that enables the user to "see" the data throughout the process.

diffmap

a program to calculate difference maps between two density maps. The maps must have the same overall dimensions and need to be aligned with each other.

Gamma

(General Approach to Magnetic resonance Mathematical Analysis) a package of C++ libraries that allow simulation of magnetic resonance (NMR, MRS) experiments. It is used for designing and analyzing NMR pulse sequences.

ESPript

(Easy Sequencing in Postscript) a utility to generate a pretty PostScript output from aligned sequences and coordinate files.

pdb-care

a tool that identifies and assigns carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported.

AQUA

a suite of programs that analyze the quality of biomolecular structures determined via NMR spectroscopy. AQUA was initially developed by Ton Rullmann and Jurgen Doreleijers at the Bijvoet Center for Biomolecular Research, Utrecht,

MOLPHY

(MOLecular PHYlogenetics) a computer program package for molecular phylogenetics.

rmeasure

a program for measuring the resolution of single-particle reconstructions.

MMC

(Metropolis Monte Carlo) a program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles employing several convergence acceleration techniques (e.g., force-biased displacement, extension-biased and local torsion changes, preferential selection of solvent to be moved, cavity-biased insertion, virial-biased volume change).

SamViewer

a 2D image display and analysis program, specifically designed for single-particle EM.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

Gorgon

an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.

Nessy

an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY autamatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models.

ACE2

a CTF Estimator. ACE2 is a completely rewritten version of ACE. ACE2 adds the additional feature of robust astigmatism estimation and CTF correction with astigmatism using either a mild Weiner filter (recommended) or phase-flipping. Since ACE2 is written in objective C, it no longer requires MATLAB to work.

TALOS-N

a tool that predicts protein backbone and sidechain torsion angles from NMR chemical shifts

WASP

a tool that searches PDB files for misidentified water molecules that should be modeled as cations.

plotutils

a GNU package containing software for programmers and technical users. Its centerpiece is libplot, a powerful C/C++ function library for exporting 2-D vector graphics in many file formats, both vector and raster. It can also do vector graphics animations. plotutils also contains command-line programs for plotting scientific data, many of which use libplot to export graphics.

CURVES

an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis.

DSSP

a program that standardizes secondary structure assignment calculated from a coordinate file. Secondary structure prediction is not supported. Designed by Wolfgang Kabsch and Chris Sander

ENTANGLE

a JAVA program that reads PDB files containing a nucleic-acid protein complex and gives a listing of interactions that occur at the interface between the nucleic-acid/protein complex and classifies these interactions into hydrogen bonds, electrostatic, hydrophobic, and Van der Waals. Entangle also recognizes when a stacking interaction occurs between two aromatic residues.

AMPS

(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.

CMView

an interactive contact map visualization and analysis tool.

WebLogo

a set of command line tools for sequence logo generation.

PDBstat

a C/C++ application developed as a coordinate and protein NMR restraint converter. This user-friendly tool provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, and analysis of atomic position consistency based on their convergence across a protein NMR ensemble.

knuspr

a tool that finds the positions of phosphates and bases in electron density maps with a fairly high degree of reliability.

surfv

a program that calculates solvent accessible area that is defined by a probe as it rolls on the surface of the molecule. Thus use of a zero radius probe will give the Van der Walls surface area.

LAFIRE

(Local-correlation-coefficient-based Automatic FItting for REfinement) an automatic refinement system for protein crystallography. The system starts with an initial model (approximate or partial model) and finishes with the final structure including water molecules. LAFIRE uses the refinement programs CNS or Refmac5.

FRODOCK

(Fast Rotational DOCKing) a tool used to efficiently generate many potential predictions of how two proteins could interact.

naccess

a stand-alone program that calculates the accessible area of a molecule from a PDB format file.

pipe2xeasy

a tool that performs conversions of spectra from NMRPipe to XEASY format. It can read the ASCII file with header information, which is produced with "showhdr -verb filename".

COMO

a program for molecular replacement calculations, using the combined molecular replacement method.

YUP

(Yammp Under Python) a molecular modeling program designed as a general purpose tool, although development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp. Also known as Yammp 2.

xv

an interactive image manipulation program for the X Window System that operates on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and (with ghostscript version 2.6 or above) it can also display them.

RnamlView

a visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView. It generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representations by rearranging various parts (e.g helices and single strands) of the RNAView 2D diagrams. RNA motifs are rapidly identified and classified with the base pair annotation and the 2D graphic display.

REPLACE

a suite of programs for molecular replacement calculations. It currently consists of two major programs, GLRF for rotation function calculations and TF for translation function calculations. In addition, a small program (ANGCAL) is a convenient tool for conversions between angles and matrices.

Mead

a program that is used for including solvation effects in biological systems, such as proteins, using an atomic model of the protein. This is done by solving the Poisson-Boltzmann equation in a dielectric medium, including distributed point charges on a grid.

Primer3

a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.

WHATIF

a general protein analysis program.

XDSi

a program that allows processing of datasets in a given directory with minimum effort when you supply it with a result directory and the directory where your frames are stored. All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed. For each dataset a space group assignment is done using POINTLESS from the CCP4 software package. Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset. A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated. You can also generate plots for datasets that have been processed using XDS without XDSi.

Note that this software requires 'kpdf' to display its output.

Burnham-Brandeis Helical Package

a suite of applications for the analysis of helical structures.

vmd-xplor

a combination of the X-PLOR structure determination program and VMD (Visual Molecular Dynamics) - a freely available molecular visualization program. This package allows manual manipulation of the protein structures to satisfy experimental NMR data, and can also be used to visualize the goodness of fit of a particular model to given restraints.

Eden

a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner.

QPack

a "quick" evaluation of steric packing in protein structures. Amino acid side chains are not represented in full atomic detail, but instead uses one or more averaged centers of interaction per residue. Side chain packing quality is determined from the spherical space available to each residue. Empirical pairwise residue contact potential can be used to estimate the correctness of model protein structures.

PLOTMTV

a multipurpose X11 plotting program that specializes in contour plots but can also handle 2D and 3D plots. The plot-types supported are: contour plots (rectangular grid, as well as triangular mesh), 2D line and scatter plots (x-vs-y), 3D surface , line and scatter plots, vector plots, probability plots, histograms, barcharts.

X3D

a boxing program developed by James Conway.

PROFphd

a program that creates fragments for Rosetta. For commercial users, Biosof LLC (www.bio-sof.com) offers additional customization and data analysis of PROFphd.

Assemble2

a Java application that allows you to design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera.

MES

(Minimal Ensemble Search) a genetic algorithm used to identify the minimal ensemble required to best fit experimental data. The simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. Written by Martin Pelikan and Michal Hammel at Lawrence Berkeley Laboratory.

SOMoRe

a 6D global search and multi-start optimization molecular replacement package.

ModelFree

a program to fit the extended model free spectral density function to NMR spin relaxation data. The program can analyze the spin-lattice relaxation rate constant (R1), the spin-spin relaxation rate constant (R2), and the heteronuclear steady-state {1H}-X nuclear Overhauser effect (NOE) for any combination of 13C and 15N spins at up to five static magnetic fields.

SURFNET

a program that generates surfaces, density contours and gap regions from coordinate data supplied in a PDB file.

RCrane

a tool that allows for semi-automated building of RNA structure within Coot.

RStudio

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

T-Coffee

a multiple sequence alignment package that can be used to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).

Aline

an interactive perl/tk application that can read common sequence alignment formats that the user can then alter, embellish, markup, etc. to produce the kind of sequence figure commonly found in biochemical articles.

XRayView

a tool that uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space.

Priism/IVE

a graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with a focus on data from 3D optical microscopy and electron tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism.

HOLE

a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels.

PyTOM

a tool that unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.

Gautomatch

a GPU-accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates.

USF Gerard Utilities

a Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.

And includes the following binaries:

• aconio
• cello
• comap
• crave
• essens
• flood
• lsqman
• mama.debug
• mapman
• mave
• moleman2
• o2d
• oops
• prof
• site2rt
• solex
• ssencs
• xpand

Staden

a set of DNA sequence assembly, editing and analyzing tools developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

AutoDock Vina

a program for drug discovery, molecular docking, and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.

R2R

a program to assist in aesthetic drawings of RNA secondary structures. It is primarily aimed at drawing consensus diagrams, but can also draw single RNA molecules.

EBSeq

a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data.

XDSAPP

a graphical user interface for processing diffraction data sets using XDS. It automates the data processing and generates graphical plots of various data set statistics provided by XDS and presenting new features of the dataset, such as radiation decay or the presence of pseudo-translational symmetry and/or twinning, using additional software. Generates intensity files suitable for CCP4, SHELX, and CNS.

ORCA

an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.

SpecView

a tool that provides a fast way to visualize NMR spectrum and peak data. It supports 2D and 3D graphical display modes for multidimensional and simple 1D spectra. Can automatically import spectra and peaks from many different file formats without user intervention. Spectra may be frequency referenced and superposed within the program.

Priism/IVE

a graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with a focus on data from 3D optical microscopy and electron tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism.

NETBLAST

a simple command-line program that allows you to submit a single file of FASTA sequences over an internet connection to the NCBI BLAST databases. Searches are submitted through the client to the NCBI servers and do not need to download the databases locally (also called netblast and blastcl3).

SCC

a suite of programs for sequence alignment: 1) aln: Pairwise alignment of biological sequences supporting spliced alignment procedures; 2) swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm; 3) prrn: global multiple alignment of a set of protein or DNA sequences by doubly-nested iterative refinement method; 4) phyln: UPGMA or NJ method to make a phylogenetic tree from a multiple alignment. 5) makmdm: constructs binary PAM matrices.

FAST ModelFree

a Perl program to assist in the analysis of laboratory frame spin relaxation data. It interfaces with ModelFree 4.01 (A. G. Palmer, Columbia University) and fully automates the process of model selection and tensor optimization.

Gautomatch

a GPU-accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates.

Eden

a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner.

Suprim

a flexible, modular software package intended primarily for the processing of transmission electron micrographs. One of several applications developed by Automated Molecular Imaging Group at The Scripps Research Institute.

MIFit

an interactive graphics application for molecular modeling, fitting, and refinement of protein structures from X-ray crystallography developed by Bradley Smith as an Open Source project while working for Rigaku/MSC Inc. A particular focus of the MIFit software is the efficient solution and analysis of protein:ligand complexes.

PARTICLE

a software package for single-particle EM image processing. It provides an integrated computing environment with comprehensive data analysis functions for particle selection, particle classification, 3D reconstruction and model evaluation. In addition, PARTICLE emphasizes on data visualization that enables the user to "see" the data throughout the process.

FRODOCK

(Fast Rotational DOCKing) a tool used to efficiently generate many potential predictions of how two proteins could interact.

Gorgon

an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.

ENTANGLE

a JAVA program that reads PDB files containing a nucleic-acid protein complex and gives a listing of interactions that occur at the interface between the nucleic-acid/protein complex and classifies these interactions into hydrogen bonds, electrostatic, hydrophobic, and Van der Waals. Entangle also recognizes when a stacking interaction occurs between two aromatic residues.

WHAT_CHECK

a protein verification tool from the WHAT IF program available as a free stand-alone program, complete with all source code.

DoGpicker

a program that sorts particles by size using the radius of a particle; it uses difference of Gaussians (DoG) for picking particles.

RnamlView

a visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView. It generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representations by rearranging various parts (e.g helices and single strands) of the RNAView 2D diagrams. RNA motifs are rapidly identified and classified with the base pair annotation and the 2D graphic display.

fpocket

an open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program.

H5ToXds

a tool used by the XDS package for the processing of EIGER HDF5 data.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

MES

(Minimal Ensemble Search) a genetic algorithm used to identify the minimal ensemble required to best fit experimental data. The simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. Written by Martin Pelikan and Michal Hammel at Lawrence Berkeley Laboratory.

Toronto Single Particle Cryo-EM Software Tool Collection

a collection of software tools for computational analysis of cryo-EM images developed by John Rubinstein/U Toronto

DireX

a tool that performs efficient geometry-based conformational sampling of protein structures under experimental restraints. It combines prior structural information with experimental data through the Deformable Elastic Network (DEN) approach which drastically reduces over-fitting.

CMView

an interactive contact map visualization and analysis tool.

Burnham-Brandeis Helical Package

a suite of applications for the analysis of helical structures.

XEASY

a program for interactive, computer-supported NMR spectrum analysis.

DelPhi

a program for calculating protein electrostatics.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Spring

(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.

FinchTV

a popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multi-pane view. And it leads the way with raw data views, BLAST searching and the ability to reverse complement sequences and traces.

randomize

a small tool to randomize phases of a 3D map in a given resolution zone. The randomization can be used to test bias in the refinement of atomic models into a map.

mag_distortion

a program used to estimate magnification distortions in electron micrographs using images of polycrystalline samples such as gold shadowed diffraction gratings. The measured distortion at a particular magnification can then be corrected in images of the sample using mag_distortion_correct. Both programs read images that are stored in MRC/CCP4 format.

mrtailor

a PDB preparation tool for use with ProSmart or for Molecular Replacement

REPLACE

a suite of programs for molecular replacement calculations. It currently consists of two major programs, GLRF for rotation function calculations and TF for translation function calculations. In addition, a small program (ANGCAL) is a convenient tool for conversions between angles and matrices.

PHASES

a program that computes phase angles for diffraction data from macromolecular crystals with programs for merging and scaling of native and derivative data sets; analyzing difference statistics; computing Patterson and electron density maps; searching for peaks; refining heavy atoms (or protein domains as rigid groups); computing phases by MIR, SIR, SAS, SIRAS, MIRAS, or from atomic coordinates for an input model; noncrystallographic symmetry averaging; combining phases from a partial structure with MIR etc phases; computation and analysis of cross difference or Bijvoet difference Fourier maps; and for phase extension and refinement.

MMTSB Toolset

(Multiscale Modeling Tools for Structural Biology) a collection of perl-based user-level utilities as well as programming libraries for multiscale protein structure modeling. Intended applications include protein structure prediction, loop modeling, structure refinement, and structure evaluation/scoring.

Matt

a multiple protein structure alignment program. It uses local geometry to align segments of two sets of proteins, allowing limited bends in the backbones between the segments.

UROX

MRC Cambridge Image Processing System

a system that determines the structure of macromolecular assemblies. The approach has been to study specimens with some form of symmetry, such as crystals or helical and icosahedral particles, using programs suitable for many kinds of 2-D and 3-D analysis.

Python Macromolecular Library

a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.

vmd-xplor

a combination of the X-PLOR structure determination program and VMD (Visual Molecular Dynamics) - a freely available molecular visualization program. This package allows manual manipulation of the protein structures to satisfy experimental NMR data, and can also be used to visualize the goodness of fit of a particular model to given restraints.

RMERGE

a tool. that calculates Rpim for merging, which HKL (scalepack) does not. There's no official manual right now but you can see Cell 147, 199-208 for more information.

naccess

a stand-alone program that calculates the accessible area of a molecule from a PDB format file.

EMIP

(EM Imaging Processing GUI) a Graphical User Interface that collects information from the user and runs existing programs from a variety of different software packages.

bin2mrc

a program to convert images saved in FEI's bin format into MRC/CCP4 format.

Primer3

a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.

plotutils

a GNU package containing software for programmers and technical users. Its centerpiece is libplot, a powerful C/C++ function library for exporting 2-D vector graphics in many file formats, both vector and raster. It can also do vector graphics animations. plotutils also contains command-line programs for plotting scientific data, many of which use libplot to export graphics.

MadBend

a program for calculating the curvature of nucleic acids. From a given list of base pair step roll, tilt and twist values, and the specification of a reference plane, the program produces the global tilt, global roll and the bend magnitude. These quantities describe the direction and magnitude of a bend angle for analysis of DNA and DNA/protein complex geometries.

SOMoRe

a 6D global search and multi-start optimization molecular replacement package.

PLOTMTV

a multipurpose X11 plotting program that specializes in contour plots but can also handle 2D and 3D plots. The plot-types supported are: contour plots (rectangular grid, as well as triangular mesh), 2D line and scatter plots (x-vs-y), 3D surface , line and scatter plots, vector plots, probability plots, histograms, barcharts.

GeFREALIGN

a version of FREALIGN modified to run on GPU processors so that the refinement process of single particle 3D reconstruction can be speedup.

Frealix

a program for the refinement of helical filament reconstructions from cryo electron micrographs. It is primarily used to process images of amyloid fibrils, though it has also been tested on TMV and actin filaments.

PROFphd

a program that creates fragments for Rosetta. For commercial users, Biosof LLC (www.bio-sof.com) offers additional customization and data analysis of PROFphd.

xv

an interactive image manipulation program for the X Window System that operates on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and (with ghostscript version 2.6 or above) it can also display them.

XDSi

a program that allows processing of datasets in a given directory with minimum effort when you supply it with a result directory and the directory where your frames are stored. All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed. For each dataset a space group assignment is done using POINTLESS from the CCP4 software package. Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset. A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated. You can also generate plots for datasets that have been processed using XDS without XDSi.

Note that this software requires 'kpdf' to display its output.

RNAView

a tool that quickly displays the secondary structure of RNA/DNA with tertiary interactions. It is fully implemented with Leontis and Westhof's ( RNA (2001) 7, 499-512), convention for the edge-to-edge hydrogen bonding interactions.

Assemble2

a Java application that allows you to design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera.

PROMALS

(PROfile Multiple Alignment with predicted Local Structure) a progressive method for aligning multiple protein sequences, with enhanced profile information from database searches and secondary structure prediction.

BOBSCRIPT

an extension to Molscript that adds sticks and spheres, stereo pictures, flexible colouring (colour ramping) and map drawing.

Curves+

a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr.

HYDROPRO

a program that computes the hydrodynamic properties of rigid macromolecules (proteins, small nucleic acids, macromolecular complexes, etc.) from their structure, as specified by the coordinates taken from a PDB file supplied by the user, from which the proper hydrodynamic model is built by the program itself.

PHOELIX

a software package for image processing of helical macromolecular complexes.

Solvate

a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations.

HYDRONMR

a program intended for the calculation of NMR relaxation of small, quasirigid macromolecules whose structure, with atomic resolution, is taken from a PDB file of atomic coordinates. HYDRONMR evaluates basic hydrodynamic quantities involved in dynamic NMR in the same fashion as HYDROPRO program, then calculates NMR quantities (T1, T2, NOE, etc) for each residue of a globular protein and reports the translational diffusion coefficient, which is available, among other sources, from some NMR experiments.

X3D

a boxing program developed by James Conway.

Swiss-PdbViewer

an application that provides a user friendly interface allowing you to analyze several proteins at the same time.

CURVES

an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis.

XDS-Viewer

an X-ray diffraction and control image viewing utility for data processed using the XDS program package.

surfv

a program that calculates solvent accessible area that is defined by a probe as it rolls on the surface of the molecule. Thus use of a zero radius probe will give the Van der Walls surface area.

d*TREK (Free)

a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors. This entry is for the free version of d*TREK.

NORMA

a software suite for the modelling of large conformational changes of 3-D protein structures under the constraint of a low resolution electron density map. Norma is used to interpret electron microscopy data using atomic scale resolution structural models and perform flexible fitting on new cases without encountering major technical difficulties.

Unblur

a tool used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format and generates frame sums that can be used in subsequent image processing.

crop

a program for cutting sections out of 2D and 3D density maps.

pipe2xeasy

a tool that performs conversions of spectra from NMRPipe to XEASY format. It can read the ASCII file with header information, which is produced with "showhdr -verb filename".

Clustal Omega

a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.

PGPLOT

a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs.

SHIFTX2

a program that predicts the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input.

PROBCONS

an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

SIGNATURE

an automated particle selection system for electron microscopy. The application was written by James Chen in Niko Grigorieff laboratory at Brandeis.

ResMap

(Resolution Map) a Python (NumPy/SciPy) application with a Tkinter GUI. It is an easy to use software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM). ResMap has a both a GUI (window) and a command line interface.

rDock

a fast, versatile and program for docking ligands to proteins and nucleic acids.

SURFNET

a program that generates surfaces, density contours and gap regions from coordinate data supplied in a PDB file.

REDCAT

a residual dipolar coupling analysis tool.

For-profit users interested in using this tool should contact Homayoun Valafar at hvalafar@gmail.com to inquire.

SCWRL3

a program for prediction of protein side-chain conformations.

pdb-care

a tool that identifies and assigns carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported.

Untangle

a program designed to separate overlapping diffraction patterns from a set of crystals with slightly different orientations. The program can read x files from the HKL Package and CCP4 MTZ files. It can output data files from which the offending reflections have been removed. A case study for a dataset from an aggregate with three dominant subcrystals can be found here.

BEST

a program for optimal planning of X-ray data collection from protein crystals.

SamViewer

a 2D image display and analysis program, specifically designed for single-particle EM.

RSRef

a program for the fitting of atomic models into electron density maps derived from x-ray crystallography or electron microscopy (EM).

YUP

(Yammp Under Python) a molecular modeling program designed as a general purpose tool, although development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp. Also known as Yammp 2.

PALES

(Prediction of ALignmEnt from Structure) a software for the analysis of residual dipolar couplings and for the prediction of the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein/nucleic acid/oligosaccharide) three-dimensional shape.

SASSIE+

a set of tools used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data plus “courtesy modules,” which include the molecular dynamics package NAMD, the scattering calculators Cryson and Crysol, and the program Hydropro for calculating hydrodynamic properties.

RSRef2000

a tool that supports real-space simulated annealing refinement with X-ray data using an electron density function that is resolution-dependent, so that it accurately models a medium resolution map. When combined with TNT’s Geometry or CNS, full stereochemical refinement is possible. It can quickly pre-refine a protein structure during or after model building, or to completely refine structures with high non-crystallographic symmetry, that have good electron density.

SSAHA2

(Sequence Search and Alignment by Hashing Algorithm) a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.

SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.

PDB_REDO

a program that refines any structural model you are working on, by optimising REFMAC refinement and by partial model rebuilding. The process is fully automated so you only need to provide an initial structure model and your reflection data.

FindDQE

a tool that determines the detective quantum efficiency (DQE) of a detector.

AMIGOS II

a tool that allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.

Dowser

a program that surveys a protein molecule's structure to locate internal cavities and assess hydrophilicity in terms of the energy of interaction of a water molecule with the surrounding atoms. Experience has shown that cavities with interaction energies below -12 kcal/mol tend to be filled, and cavities for which the energy is above that threshold, tend to be empty.

summovie

a tool that uses the alignment results from the software application Unblur to calculate movie frame sums.

QPack

a "quick" evaluation of steric packing in protein structures. Amino acid side chains are not represented in full atomic detail, but instead uses one or more averaged centers of interaction per residue. Side chain packing quality is determined from the spherical space available to each residue. Empirical pairwise residue contact potential can be used to estimate the correctness of model protein structures.

TALOS-N

a tool that predicts protein backbone and sidechain torsion angles from NMR chemical shifts

iMOD (NMA)

a toolkit to perform Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic structures. Vibrational analysis, motion animations, morphing trajectories and Monte-Carlo simulations can be easily carried out at different scales of resolution using this toolkit.

COMO

a program for molecular replacement calculations, using the combined molecular replacement method.

rmeasure

a program for measuring the resolution of single-particle reconstructions.

VEDA

a visual environment developed to fit interactively atomic models into 3D reconstructions. Calculations are performed in reciprocal-space and the symmetry of the reconstruction is taken into account. The computations are fast and an entire EM reconstruction can be used.

IPLT

(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk.

Wattos

a collection of Java programs for structural biology and NMR spectroscopy that analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors worldwide into the PDB and BMRB.