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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.
a versatile, integrated software system for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures.
an Any-to-PostScript filter that processes plain text files, but also pretty prints quite a few popular languages.
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.
a heavily optimized molecular dynamics (MD) engine specially designed to run on NVIDA GPUs. It is extremely fast (115ns/day for DHFR using 1 GPU) and performs MD simulations on the microsecond scale in a single workstation. ACDMD can read CHARMM/NAMD and AMBER input files, works with CUDA and OpenCL, and uses similar syntax to other MD software. ACEMD is freely available to ...
displays protein crystallography X-ray diffraction data. The data may be displayed as a 2-D image, 3-D wire mesh or as integer pixel values. Data files may be saved in tiff or postscript format.
consists of the standalone program ALBULA VIEWER, 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.
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.
a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. Alscript does not support point-and-click, but has a scripting language to allow complex effects.
consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models
allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.
(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.
a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.
a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE). This software was written by Nathan Baker in collaboration with J. Andrew McCammon and Michael Holst and enhanced by several others.
a "pipeline" for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images or particle stacks using a set of provided tools. Appion consists of a web-based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed ...
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, The Netherlands. Current maintenance and expansion by Jurgen Doreleijers, BioMagResBank, University of Wisconsin-Madison, USA.
the structure-solution program that constitutes a general crystallographic Ab Initio macromolecular phasing method for 2Å data, based on the combination of location of model fragments like small α-helices with PHASER and density modification with SHELXE.
(Ambiguous Restraints for Iterative Assignment) a software that automates NOE assignment and NMR structure calculation.
An interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.
At the request of the developer, this software is licensed on a per-user basis. To enable ARP/wARP license in the SBGrid environment, each user should:

- visit the ARP/wARP website.
- download any of the current versions via your web browser.
- in the shell run 'sbgrid-register -r path/to ...
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.
a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.

ATSAS is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register here http://www.embl-hamburg.de/biosaxs/atsas-online/register.php, then send a copy of your registration confirmation to us at licensing@sbgrid.org ...
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).
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.
a program for drug discovery, molecular docking, and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.
combines third-party processing programs with new tools for automated data processing of single-sweep, multi-sweep and multi-crystal X-ray diffraction data.
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.
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.
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.
a program for optimal planning of X-ray data collection from protein crystals.

BEST is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register here http://www.embl-hamburg.de/BEST/download_request3.1.html, then send a copy of your registration confirmation to us at licensing@sbgrid.org.
a program for filtering 3D maps and applying B-factors.
a program to convert images saved in FEI's bin format into MRC/CCP4 format.
a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
a set of tools for biological computation written in Python by an international team of developers.
a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data. User guides are available from:
  • Official RAW tutorial ...
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.
a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
(Buffalo n' Pittsburgh Interface) for complete protein phasing; combines SnB and the Phases Suite.
an extension to Molscript that adds sticks and spheres, stereo pictures, flexible colouring (colour ramping) and map drawing.
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.
a collection of programs and a platform for the development of software for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image and molecular processing.
a suite of applications for the analysis of helical structures.
a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.

(Computer Aided Resonance Assignment) an application for the analysis of NMR spectra and computer-aided resonance assignment.
a software tool for the analysis and visualisation of tunnels and channels in protein structures. This is the command line version and not the PyMOL plugin version.
a software tool for the calculation, analysis, and real-time visualization of access tunnels and channels in static and dynamic protein structures with an intuitive GUI.
(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography. All SBGrid members must complete the CCP4 license and return the executed document directly to The Science and Technology Facilities Council as specified on the CCP4 licensing page located here: http://www.ccp4.ac.uk/ccp4license.php.
offers a quick and easy way to create beautiful publication quality images and movies and to superpose and analyze structures.
an analysis program built on top of the CCP Data Model, inspired partly by the program ANSIG (Per Kraulis) and partly by the program Sparky (T.D.Goddard and D.G.Kneller, UCSF).
a graphical tool to construct chemical compound definitions for NMR, created to handle concepts like protonation variants and magnetic equivalence that are required for NMR resonance assignment. Several different chemical file formats are supported, including PDB, .mol and .mol2, but ChemBuild is special in its ability read and write CCPN chemical component XML files, which store NMR-aware information.
a highly extensible, interactive molecular graphics program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. It is often a tool of choice for rendering EM volumes.
a general purpose multiple sequence alignment program for DNA or proteins.
a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
an interactive contact map visualization and analysis tool.
(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement.
a program for molecular replacement calculations, using the combined molecular replacement method.
a method to generate protein conformations around a known structure based on geometric restrictions.
(Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.
a program for non-linear least squares fitting of CPMG relaxation dispersion curves.
a program for cutting sections out of 2D and 3D density maps.
a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.
(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.
CTFFIND3 and CTFTILT are two programs for finding CTFs of electron micrographs.
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.
an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis.
a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr.
a program for the automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR.

CYANA is a commercial software application that we can include in your installation for ease of use, but that requires you or your institute to have a current license in place. To enable the SBGrid installation for CYANA please send an email to licensing@sbgrid.org ...
an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself. cython is installed as a module within python.
a program for calculating protein electrostatics.

DelPhi is freely available to non-profit labs, but each lab must register with Columbia before we can install the software. To include this software in your installation, please register here https://bhapp.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi, then send a copy of your registration confirmation to us at licensing@sbgrid.org.

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images designed to cope with the ever increasing volumes and rates of data collection, and with the developments in experimental methodology, from shutterless, fine-sliced rotation scans through to the randomly-oriented snapshots of serial crystallography. This software utilizes techniques of parallel processing using multiple CPU and GPU machines, facilitating not ...
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.
a realtime 3D visualization program for structural biology data.
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.
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.
a program that sorts particles by size using the radius of a particle; it uses difference of Gaussians (DoG) for picking particles.
a program that surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of those cavities 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 ...
(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.
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
a software program for Defining the Secondary Structures of RNA from three-dimensional coordinates.
a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

d\*TREK is a commercial software application that we can include in your installation for ease of use, but that requires you or your institute to have a current license in place. To enable the SBGrid installation for d\*TREK please send an email to licensing@sbgrid ...
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, contains neither the Reqab absorption correction nor the absorption correction written by Higashi. It also does not make any use of collision file information during the strategy generation.
a software environment for subtomogram averaging of cryo-EM data.
a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.
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. Unlike the original DynDom (DynDom1D), this method is blind to atomic bonding and atom type and can, therefore, be applied to biomolecular complexes containing different constituent molecules such as protein, RNA or ...
a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data.
a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner.
(ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography.
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.
a program to convert images from/to formats used in the "electron microscopical community" (3DEM)
a suite of scientific image processing tools with a particular focus on single particle reconstruction and which includes Foldhunter and Helixhunter.
EMAN2 is a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications. MPI use : to use MPI-enabled executable in SBGrid's EMAN2, use the mpirun.eman2 executable. This will use the older 1.6.3 version of MPI required by EMAN2/SPARX.
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). The program accepts 3D maps in any common EM format and accepts FSC curves in the format of most common packages for single particles, cryoEM. As output, the program produces a sharpened map and the Guinier plot that allows assessment ...
integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
(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.
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. These interactions are then classified into hydrogen bonds, electrostatic, hydrophobic, and Van der Waals. Entangle also recognizes when a stacking interaction occurs between two aromatic residues. In addition to a listing, Entangle allows the user to ...
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.
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.

ESCET is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register here http://www-db.embl ...
(Easy Sequencing in Postscript) a utility to generate a pretty PostScript output from aligned sequences and coordinate files.
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
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.
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.
FinchTV is the 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.
determines the detective quantum efficiency (DQE) of a detector.
fpocket is a very fast 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.
(Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.
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.
(Fast Rotational DOCKing) a tool used to efficiently generate many potential predictions of how two proteins could interact.
(Function and Data Analysis) a program whose nmrPipeFit component is designed to analyse nD (n>1) NMR correlation spectra. The program is currently designed for arrayed 2D spectra, such as relaxation experiments and diffusion experiments, and simple 2D and 3D spectra.
(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.
a GPU-accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates.
a GPU accelerated program for accurate and robust, real-time CTF determination of EM Micrographs.
a version of FREALIGN modified to run on GPU processors so that the refinement process of single particle 3D reconstruction can be speedup.
a powerful and comprehensive suite of molecular biology tools. SBGrid members from academic/non-profit laboratories share a 10-seat license for this suite of tools.
a GPU-enhanced version of RELION that dramatically speeds up 2D/3D classification and 3D auto-refine.
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.
creates a Globus endpoint on your laptop or other personal computer and allows you to transfer and share files, regardless of whether you have administrative privileges on your machine. Globus Connect Personal is available for Mac OS X and Linux operating systems.
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.
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.
a general plotting, curve fitting and data transformation program.
an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php
a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.
a modular program for SPM (scanning probe microscopy) data visualization and analysis.
used by the XDS package for the processing of EIGER HDF5 data.
(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.
a program suite (hbplus, access and clean) to compute hydrogen positions, hydrogen bonds, and neighboring interactions. The application was developed at University College London.
a data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection strategy and processing data. HKL is based on the extended versions of Denzo, Xdisplayf and Scalepack.HKL was developed and is maintained by Wladek Minor (University of Virginia).

HKL2000 is a commercial software application that we can include in your installation for ease of use, but that ...
a graphical user-interface for macromolecular phasing. HKL2MAP is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register [here][1], then send a copy of your registration confirmation to us at licensing@sbgrid.org . [1]: http://webapps.embl-hamburg.de/bundle/download.php?hkl2mp=true&sitcom=false
a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels. The application was developed by Oliver S. Smart, and is currently hosted by the Sansom Laboratory at the University of Oxford.
a computer 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. The basic hydrodynamic quantities involved in dynamic NMR are evaluated in the same fashion as in the closely related HYDROPRO program. HYDRONMR then calculates NMR quantities, like T1, T2, NOE,. for each residue of a globular ...
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. The HYDROPRO calculation comprises the basic hydrodynamic properties: translational diffusion coefficient, sedimentation coefficient, intrinsic viscosity, and relaxation times, along with the ...
a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data.
a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
a user-friendly extension to Ed Egelman's Iterative Helical Real Space Reconstruction (IHRSR) software. It includes all of the original IHRSR functionality plus the capabilities to determine out-of-plane tilt, apply dihedral symmetry, and automatically construct a starting model from the image data. IHRSR++ also contains a number of Perl and Spider scripts for performing common preprocessing and data manipulation tasks such as power spectra ...
a simple, user-friendly tool for image classification and segmentation in up to three spatial and one spectral dimension. Using it requires no experience in image processing.
a public domain Java image processing program inspired by NIH Image for the Macintosh. It 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". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image ...
a software suite to create, edit, compose, or convert bitmap images.
a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates.
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.
a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package.
(Integrative Modeling Platform) designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.
(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk.
provides a architecture for interactive computing with a browser-based notebook where you can combine code, text, mathematical expressions, inline plots, and other rich media into a single document and support for interactive data visualization. IPython is now part of the larger Jupyter project. Please see the [Jupyter website](http://jupyter.org/index.html) for more information. IPython is installed as a module within python ...
an algorithm to reconstruct non-uniformly acquired NMR data.
a multiple sequence alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.
finds the positions of phosphates and bases in electron density maps with a fairly high degree of reliability.
(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.
a system designed for automated collection of images from a transmission electron microscope; it includes the python-side programs written in python and c, the MySQL database and server, and the mainly php-based image and data viewers on a web server.
a program for automatically plotting protein-ligand interactions.
a graphical front-end to the LIGPLOT (protein-ligand interactions) and DIMPLOT (protein-protein, domain-domain interactions) programs. The plots generated by these programs can be interactively edited on screen, superposed and printed.
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 thus describe the direction and magnitude of a bend angle and can be used to analyze DNA and DNA/protein complex ...
a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
mag_distortion_estimate is 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.
a model building application for X-ray crystallography.
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.
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.
an application that assists in the processing and curation of macromolecular structure data.
(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.
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.
(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.
a software package comprised of AutoDockTools (ADT), Python Molecule Viewer (PMV) and a python programming environment called Vision, developed for visualization and analysis of molecular structures.

AutoDockTools is graphical front-end for setting up and running AutoDock - an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

PMV is a powerful ...

an expert system for running molecular replacement and refinement applications, and analyzing the data obtained from high-throughput co-crystallography and fragment screening projects. MIExpert is a module of 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.
(Mixture of Isoforms model) for isoform quantitation using RNA-Seqis a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. MISO is installed as a standalone program and as a module within python.
(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).
(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.
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.
used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various ...
a novel program developed to allow the determination of alignment tensor parameters for individual or multiple domains in macromolecules from residual dipolar couplings and to facilitate their manipulation and construct low-resolution models of macromolecular structure.
a universal toolkit for rapid and fully 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. MOLE is a powerful software program for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories in which analysis of a large number of ...
a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules.
(MOLecular PHYlogenetics) a computer program package for molecular phylogenetics.
a protein structure analysis platform offering quality validation for 3D structures of proteins, nucleic acids and complexes.
one of the most popular programs for the generation of publication-quality figures.
a package for processing film and image plate data.
a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images. MotionCor2 runs on a Linux platform equipped with one or more advanced NVIDIA GPU cards. It ...
a program that corrects whole frame image motion recorded with dose fractionated image stacks.
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.
a PDB preparation tool for use with ProSmart or for Molecular Replacement
(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.
a stand-alone program that calculates the accessible area of a molecule from a PDB format file.
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
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.
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.
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).
a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. This is the official NMRScience version of NMRPipe.
used to visualize and Analyze Nuclear Magnetic Resonance Data.
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. A typical application for this software is the interpretation of electron microscopy data using atomic scale resolution structural models. The software package provided here should enable the interested user to perform flexible fitting on new cases without encountering major technical ...
a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.
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.
contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. NumPy is installed as a module within Python.
a model building application for X-ray crystallography.
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.
a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.
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.
(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.
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.
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.
a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: Adding a limited number of missing heavy atoms to biomolecular structures; Determining side-chain pKas; Placing missing hydrogens; Optimizing the protein for favorable hydrogen bonding; Assigning charge and radius parameters ...
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.
an easy to use application that fixes problems in Protein Data Bank files in preparation for simulating. Fixes include: adding missing heavy or hydrogen atoms, building missing loops, convert non-standard residues to their standard equivalents, deleting unwanted heterogens or chains from the model, and building a water box for explicit solvent simulations.
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.
a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well ...
a set of tools used by the PDB for processing and checking structure data.
(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.
(Pathologically Eclectic Rubbish Lister or sometimes called the Practical Extraction and Reporting Language) a highly capable, feature-rich family of programming languages.
performs orientation searches and positional refinement of icosahedral viruses.
a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs.
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 ...
(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
a linear-scaling, semiempirical quantum mechanics (SE-QM) program DivCon with the Phenix X-ray refinement engine. Phenix/DivCon does not utilize CIF(s), link restraints and other refinement parameters so there are fewer assumptions about the model. Accurate energy and density scoring tools also allow tautomer/protomer and “flip state” determination.
a software package for image processing of helical macromolecular complexes.
a free package of software programs for inferring phylogenies.
performs conversions of spectra from NMRPipe to XEASY format. Pipe2xeasy can read the ASCII file with header information, which is produced with "showhdr -verb filename".
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. The program has an rough but functional Graphical User Interface, through which it is possible ...
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. libplot is device-independent in the sense that its API (application programming interface) does not depend on the type of graphics file to be exported ...
a newly designed NMR chemical shift guided protein structure alignment method to generate protein templates with the best matched local structure from the Protein Data Bank. It is based on experimental input data comprising 13Cα, 13Cβ, 13C', 15N, 1Hα, and 1HN NMR chemical shifts, plus sparse NOEs if available, and directly exploits the powerful bioinformatics algorithms previously developed for sequence-based homology modeling.
(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.
the 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.
a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.
an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.
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.
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.
a protein structural dynamics analysis software package. ProDy is installed as a module within python.
the ultimate protein least squares fitting program.
creates fragments for Rosetta. For commercial users, Biosof LLC (www.bio-sof.com) offers additional customization and data analysis of PROFphd.
(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.
a threading-based protein structure prediction system.
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.
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).
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST. PSIPRED is freely available to all users, but each lab must download the software from the PSIPRED website before we can install the software. To include this software in your installation, please download the software here http://bioinfadmin.cs.ucl.ac ...
widely used molecular visualization package developed by Warren DeLano, and now maintained by Schödinger, LLC. SBGrid non-profit laboratories have full access to the official incentive builds of PyMOL. The SBGrid Consortium PyMOL license credentials are contained in the NOTES file in the PyMOL installation directories in your software installation.
an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API and 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.
a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C++ or Java, thus overall, allowing programmers to work more quickly and integrate their systems more effectively. Python includes the following scientific modules: Appion, Cython, iPython Notebook, Miso, NumPy, Pandas, ProDy ...
a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
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.
cross platform time zone library that brings the Olson tz database into Python and allows accurate and cross platform timezone calculations using Python 2.4 or higher. It also solves the issue of ambiguous times at the end of daylight saving time, which you can read more about in the Python Library Reference (datetime.tzinfo).
software for macromolecular electrostatics. Qnifft is available to academic users, but each lab must download the software from the Qnifft website before we can install the software. To include this software in your installation, please download the software here http://crystal.med.upenn.edu/software.html, then send us an email at licensing@sbgrid.org.
a "quick" evaluation of steric packing in protein structures. Amino acid side chains are not represented in full atomic detail. Instead, one or more averaged centers of interaction per residue are used. A measure of the quality of side chain packing is determined from the available spherical space available to each residue. Additionally, an empirical pairwise residue contact potential can be used to estimate ...
detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.
a comprehensive, platform-independent, user-friendly, and complete software package that enables efficient, reliable, highly automated, and accurate analysis of high-throughput capillary electrophoresis-detected nucleic acid chemical probing experiments.
a free software environment for statistical computing and graphics.
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.
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.
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.
(Protein NMR backbone resonance assignment) uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. This enables rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins. RASP takes as input spin systems assembled on the basis of an arbitrary set of conventional triple-resonance NMR experiments. Uniquely, RASP is capable ...
a set of tools for generating high quality raster images of proteins or other molecules.
allows for semi-automated building of RNA structure within Coot.
a fast, versatile and program for docking ligands to proteins and nucleic acids.
a residual dipolar coupling analysis tool. For-profit users interested in using this tool should contact Homayoun Valafar at hvalafar@gmail.com to inquire.
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.
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. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc ...
a software package designed for the study of molecular dynamics by NMR data analysis.
(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.
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).
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.
(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.
a program to detect molecular motions by automatic electron density sampling.
a program for measuring the resolution of single-particle reconstructions.
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.
a visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView (above). The application generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representation desired by the user 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 ...
a complete package for RNA and DNA secondary structure prediction and analysis.
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.
a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.
(RNA Structure Framework) is a modular toolkit developed to deal with RNA structure probing high-throughput data, from reads mapping to structure deconvolution. This software has been superseded by RNA Framework (http://www.rnaframework.com).
a program for the fitting of atomic models into electron density maps derived from x-ray crystallography or electron microscopy (EM).
supports real-space simulated annealing refinement with X-ray data. RSRef uses 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. RSRef can be used to quickly pre-refine a protein structure during or after model building, or to completely refine structures with high non-crystallographic symmetry ...
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.
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.
(Sequence Alignment and Modeling system) a collection of tools for creating, refining, and using linear hidden Markov models for biological sequence analysis.
(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.
a 2D image display and analysis program, specifically designed for single-particle EM.
a program suite used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data.

SASSIE is available in the SBGrid suite in two different variations, with courtesy modules (SASSIE+) without (SASSIE). The courtesy modules include the ATSAS applications Cyrson and Crysol, which have additional licensing requirements. If you would like the SASSIE version including courtesy ...
the program suite SASSIE (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.
a plotting facility for SAXS-data, as well as a convenient tool to quickly generate plots for publication. Saxsview shows 1D-data in .dat, .int, .fit and .fir formats of the ATSAS package, the cansas .xml format (v1.0), as well as .csv files.
a JAVA-based application for basic analysis of SAXS datasets. Scatter is developed by Robert Rambo at the Diamond Light Source (Didcot, UK). The program was previously developed at the SIBYLS beamline (12.3.1) of the Advanced Light Source, Berkeley, CA.
a suite of programs for sequence alignment including: aln, swg, prrn, phyln and makmdm. aln: Pairwise alignment of biological sequences supporting spliced alignment procedures. swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm. Currently spliced alignment is not supported. Profile version is very slow. prrn: global multiple alignment of a set of protein or DNA sequences by doubly nested iterative ...
a suite of tools for small molecule drug discovery. The Schrodinger Suite runs on Linux and Mac workstations, but due to it’s size, it is not included in our default installation. To add Schrördinger to your installation, please email bugs@sbgrid.org. Use of the Schrodinger Molecular Modeling Suite through SBGrid is limited to nonprofit groups located in the US and Canada. Members ...
an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.
(pronounced “Sigh Pie”) a Python-based ecosystem of open-source software for mathematics, science, and engineering. In particular, these are some of the core packages: NumPy, SciPy Library, Matplotlib, IPython, Sympy, pandas
an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures.
a program for prediction of protein side-chain conformations.
a program for prediction of protein side-chain conformations.
converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides extensive diagnostic information useful for experiment analysis and troubleshooting.
an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the substructure determination program SHELXD, the density modification program SOLOMON and the model building programs BUCCANEER and ARP/wARP. It allows fully automated structure solution by experimental phasing, from merged reflection data to an initial model, without any user intervention.
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. SHELX was written and is actively ...
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. SHELX was written and is actively ...
a program that rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. SHIFTX uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects).
predicts the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input.
an automated particle selection system for electron microscopy. The application was written by James Chen in Niko Grigorieff laboratory at Brandeis.
(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).The SIMPLE back-end consists of an object-oriented numerical library with a single external dependency - the Fastest Fourier Transform in the West (FFTW). The SIMPLE front-end consists of a few standalone, interoperable components developed according to the 'Unix ...
a collection of utilities designed to help setting up and analyze molecular simulations.
a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies.
(Sparse Multidimensional Iterative Lineshape Enhanced) a NMRPipe processing function whose algorithm integrates a priori information about NMR signals for most robust reconstruction of non-uniformly sampled (NUS) multidimensional data.
based on Shake-and-Bake (a dual-space direct-methods procedure), a computer program for the determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites.
a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations. Solvate generates irregularly-shaped solvent volumes, adapted to a given solute's structure; allows efficient computation of boundary forces as required in molecular dynamics simulations; guarantees a minimal solute-boundary-distance; allows to specify a minimum solvent surface curvature in order to avoid `flat' surface ...
a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.
6D global search and multi-start optimization molecular replacement package.
a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.
(single particle analysis for resolution extension) an image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment.
CcpNmr SpecView is designed to provide a fast way to visualise NMR spectrum and peak data. It supports 2D and 3D graphical display modes for multidimensional and simple 1D spectra. SpecView can automatically import spectra and peaks from many different file formats without user intervention. Spectra may be frequency referenced and superposed within the program.
SPHIRE is a new software suite designed for easy access to cryo electron microscopy with the clear goal of quality assessment and result reproducibility by statistical resampling. While being well suited for cryo-EM novices, experienced users will find comfort in the accessibility of almost every possible variable in advanced option tabs and the transparent, easily customizable Python-based framework for non-standard processing pipelines. In a ...
(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.
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.
(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.
(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.
a set of DNA sequence assembly, editing and analyzing tools. Developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
(STructural Alignment of Multiple Proteins) a suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. The software will also search a database of protein structures to identify structurally similar proteins. The suite includes a number of utility programs for the ...
uses the alignment results from the software application Unblur to calculate movie frame sums.
a pipeline that uses data obtained from ShapeMapper to model RNA secondary structures, including pseudoknots; identify de novo regions with well-defined and stable structures; and visualize most probable and alternative helices.
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.
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.
a program that generates surfaces, density contours and gap regions from coordinate data supplied in a PDB file.
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.
an application that provides a user friendly interface allowing you to analyze several proteins at the same time.
predicts protein backbone and sidechain torsion angles from NMR chemical shifts
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).
a program that allows the determination of rotational diffusion from three-dimensional structure coordinates and experimental 15N relaxation data, and now allows a rigorous model-free analysis of local internal mobility affecting backbone amides, from 15N {R1,R2,nOe} relaxation rates in the presence of an isotropic or anisotropic rotational diffusion tensor.
a program for the simultaneous superpositioning and analysis of multiple macromolecular structures via the method of maximum likelihood (ML).
offers protein fold recognition by optimal protein sequence threading. THREADER is freely available to non-profit labs, but each lab must register with University College London before we can install the software. To include this software in your installation, please register here http://bioinf.cs.ucl.ac.uk/web_servers/psipred_server/obtain_threader_3_licence, then send a copy of your registration confirmation to us at licensing@sbgrid.org.
an open source suite of classes and programs implemented in C++ for single particle electron microscopic image processing.
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.
a Python-based program package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems.
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.
a collection of software tools for computational analysis of cryo-EM images developed by John Rubinstein/U Toronto
a software package for comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments.
a comprehensive data analysis software package for hydrodynamic data from analytical ultracentrifugation experiments. It is the latest multi-platform version of UltraScan, which replaced the UltraScan II distribution. UltraScan II development has stopped although it is still available. Please note that if you want to view legacy data from UltraScan II, you will still need to install UltraScan II, since UltraScan III is not backward ...
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.
performs automated NMR data analysis for protein 3D structure determination. UNIO represents the result of more than a decade of innovative research performed in order to enable accurate, objective and highly automated protein structure determination by NMR.
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.
designed for interactive fitting of high-resolution X-Ray crystallography models into Electron Microscopy reconstructions. It can also be used to fit two maps together (e.g., in tomography) or to perform Normal-modes calculations. UROX is deprecated, a new version named VEDA should be used instead.
the 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
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.
a slightly vectorized (AVX & SSE instructions) version of the original RELION 1.4 code by Dmitry Tegunov of the Max Planck Institute.
a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
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. vmd-xplor is freely available to non-profit labs, but each lab must register with ...
searches PDB files for misidentified water molecules that should be modeled as cations.
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.
command line tools for sequence logo generation.
the protein verification tool from the WHAT IF program available as a free stand-alone program, complete with all source code.
a general protein analysis program.
a boxing program developed by James Conway.
used for processing electron diffraction data. Previously available only on DEC Alpha.
a two-dimensional molecule drawing program for Unix operating systems that can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.
(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.
a graphical user interface for the easy and convenient processing of diffraction data sets using XDS. It is available for all our experimental end-stations. It automates the data processing and generates graphical plots of various data set statistics provided by XDS. By incorporating additional software, further information on certain features of the dataset, such as radiation decay or the presence of pseudo-translational symmetry and ...
a program for generating delta-CC1/2 values, for individual frames, or groups of frames, from a single dataset collected with the rotation method and processed by XDS.
a GUI (graphical user interface) for XDS designed to help both novice and experienced users; it enable XDS data processing without the command line and supplies additional graphical information in a simple, user-modifiable and user-extensible way. It graphically displays the ASCII and cbf files that XDS writes and can run useful shell commands with a simple mouse click.
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 ...
a collection of python scripts made to simplify the processing of crystal diffraction images with the XDS Program Package. Provided that the diffraction parameters are well recorded in the diffraction image headers, XDS data processing can be started with a simple command lines (see manual for details).
a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.
an X-ray diffraction and control image viewing utility for data processed using the XDS program package.
a program for interactive, computer-supported NMR spectrum analysis.
an expert system for automated reduction of X-Ray diffraction data from macromolecular crystals, making use of existing software (CCP4, XDS, Phenix, CCTBX.) XIA2 is now included with DIALS.
(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.
a generalized package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was originally derived from XPLOR version 3.851 and contains all of the functionality therein while also incorporating numerous completely new features designed to render its overall architecture highly flexible and to foster the rapid and easy development of new and improved functionality. This architecture is ...
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.
an interactive image manipulation program for the X Window System. It can operate 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 if you have ghostscript (version 2.6 or above) installed on your machine, it ...
(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.
a full rigid-body search of docking orientations between two proteins.
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. Zephyr was written (is being written) by Alex Stewart and Donald J. Olbris in the laboratories of Prof. David J. DeRosier and Prof. Niko Grigorieff at the Rosenstiel Basic Medical Sciences Research Center at Brandeis University ...
a free database of commercially-available compounds for virtual screening. ZINC contains over 21 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).
a subset of chemical compounds that are used for screening at the ICCB-Longwood Screening Facility. The dataset was compiled by David Wrobel (ICCB-Longwood) for in silico docking. The date-stamped datasets are available in /programs/share/iccb.