Software Updates

adxv

a tool that 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.

VMD

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

ULTRASCAN3

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.

Dynamo

a software environment for subtomogram averaging of cryo-EM data.

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

DENSS

(DENsity from Solution Scattering) an algorithm used for calculating ab initio electron density maps directly from solution scattering data.

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.

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.

NAMD

a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

MUSCLE

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

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.

MPICH

a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.

MOSFLM

a package for processing film and image plate data.

Molprobity

a protein structure analysis platform offering quality validation for 3D structures of proteins, nucleic acids and complexes.

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.

MISO

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.

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.

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.

Maxit

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

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.

knuspr

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

Jalview

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.

istHMS

an algorithm to reconstruct non-uniformly acquired NMR data.

IPLT

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

iMosflm

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

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

ImageMagick

a software suite to create, edit, compose, or convert bitmap images.

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.

HOLE

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

HKL2MAP

a graphical user-interface for macromolecular phasing.

HHsuite

an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

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.

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

Grace

a general plotting, curve fitting and data transformation program.

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.

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.

Ghostscript

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

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.

FREALIGN

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

Focus

an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.

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.

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.

FASTA

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

ESPript

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

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.

EMBOSS

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

em2em

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

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).

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.

DynDom

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

DSSR

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

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

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.

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.

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.

DINO

a realtime 3D visualization program for structural biology data.

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.

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.

CTF

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

CrystFEL

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.

crop

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

CONCOORD

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

CNS

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

CMView

an interactive contact map visualization and analysis tool.

Clustal

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

CCP4mg

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

CARA

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

Burnham-Brandeis Helical Package

a suite of applications for the analysis of helical structures.

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.

CellProfiler

a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

Bsoft

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.

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.

BLAST

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

bfactor

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

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.

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.

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.

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).

ARP/wARP

an interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.

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.

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.

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.

ULTRASCAN2

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

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.

SHELX-2013

a set of programs for macromolecular phasing. SHELXC provides a simple and fast way to set 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.

OpenJDK

(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).

Situs

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.

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.

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.