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Name Description Keywords Links  
a versatile, integrated software system for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures. Keywords: struct-analysis, struct-vis, nucleic-acids,
an Any-to-PostScript filter that processes plain text files, but also pretty prints quite a few popular languages. Keywords: utilities
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. Keywords: bioinformatics
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. Keywords: bioinformatics
allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures. Keywords: nucleic-acids
(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching. Keywords: bioinformatics
a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis. Keywords: struct-analysis Py-module, utilities,
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. Keywords: struct-analysis
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. Keywords: struct-analysis,
(Ambiguous Restraints for Iterative Assignment) a software that automates NOE assignment and NMR structure calculation. Keywords: sb,
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. Keywords: nucleic-acids sva,
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 ...
Keywords: saxs
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. Keywords: sb,
combines third-party processing programs with new tools for automated data processing of single-sweep, multi-sweep and multi-crystal X-ray diffraction data. Keywords: 2d-crystallograp,
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. Keywords: bioinformatics
a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. Keywords: utilities
a set of tools for biological computation written in Python by an international team of developers. Keywords: utilities
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 ...
Keywords: saxs
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. Keywords: bioinformatics ChIP-Seq, RNA-Seq,
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. Keywords: bioinformatics ChIP-Seq, RNA-Seq,
an extension to Molscript that adds sticks and spheres, stereo pictures, flexible colouring (colour ramping) and map drawing. Keywords: struct-vis
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. Keywords: bioinformatics
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. Keywords: struct-analysis
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. Keywords: struct-vis
(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. Keywords: sb,
offers a quick and easy way to create beautiful publication quality images and movies and to superpose and analyze structures. Keywords: struct-vis
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. Keywords: struct-vis, sb,
a general purpose multiple sequence alignment program for DNA or proteins. Keywords: bioinformatics
a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Keywords: bioinformatics
an interactive contact map visualization and analysis tool. Keywords: struct-analysis struct-vis,
(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement. Keywords: sb,
(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. Keywords: struct-vis,
CTFFIND3 and CTFTILT are two programs for finding CTFs of electron micrographs. Keywords: sb,
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. Keywords: sb,
an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis. Keywords: struct-analysis nucleic-acids,
a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr. Keywords: struct-analysis nucleic-acids,
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. Keywords: Py-module
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.

Keywords: struct-analysis
a realtime 3D visualization program for structural biology data. Keywords: struct-vis
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. Keywords: struct-analysis
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 ... Keywords: struct-analysis
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 Keywords: struct-analysis
a software program for Defining the Secondary Structures of RNA from three-dimensional coordinates. Keywords: struct-analysis
a software environment for subtomogram averaging of cryo-EM data. Keywords: tomography,
a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available. Keywords: struct-analysis
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 ... Keywords: struct-analysis
a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data. Keywords: Bioconductor bioinformatics, RNA-Seq,
(ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography. Keywords: tomography
a suite of scientific image processing tools with a particular focus on single particle reconstruction and which includes Foldhunter and Helixhunter. Keywords: sb,
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. Keywords: struct-vis, sb,
integrates a range of currently available packages and tools for sequence analysis into a seamless whole. Keywords: bioinformatics utilities,
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 ... Keywords: struct-analysis nucleic-acids,
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. Keywords: sb,
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 ...
Keywords: struct-analysis
(Easy Sequencing in Postscript) a utility to generate a pretty PostScript output from aligned sequences and coordinate files. Keywords: bioinformatics
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples. Keywords: bioinformatics
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. Keywords: utilities
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. Keywords: bioinformatics
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. Keywords: struct-analysis
(Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. Keywords: sb,
a version of FREALIGN modified to run on GPU processors so that the refinement process of single particle 3D reconstruction can be speedup. Keywords: sb,
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. Keywords: bioinformatics
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command. Keywords: utilities
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. Keywords: utilities
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. Keywords: utilities
a general plotting, curve fitting and data transformation program. Keywords: utilities
an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php Keywords: utilities
a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids. Keywords: sb,
(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. Keywords: struct-analysis, sb,
a program suite (hbplus, access and clean) to compute hydrogen positions, hydrogen bonds, and neighboring interactions. The application was developed at University College London. Keywords: struct-analysis
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. Keywords: struct-analysis
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 ... Keywords: struct-analysis
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. Keywords: bioinformatics ChIP-Seq, DNA-Seq,
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. Keywords: utilities
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 ... Keywords: utilities,
a software suite to create, edit, compose, or convert bitmap images. Keywords: utilities
an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates. Keywords: sva,
("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA ... Keywords: bioinformatics genomics,
(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk. Keywords: 2d-crystallograp
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 ... Keywords: Py-module
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. To use Jalview on OS X, you will need to install Java: * Keywords: bioinformatics
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. Keywords: bioimage
a program for automatically plotting protein-ligand interactions. Keywords: struct-analysis
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. Keywords: struct-analysis
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 ... Keywords: struct-analysis nucleic-acids,
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). Keywords: bioinformatics
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. Keywords: struct-analysis
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. Keywords: struct-analysis struct-vis,
an application that assists in the processing and curation of macromolecular structure data. Keywords: struct-analysis
(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. Keywords: struct-analysis
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. Keywords: struct-analysis
(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. Keywords: saxs
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 ...

Keywords: struct-vis sb,
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. Keywords: struct-vis,
(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. Keywords: bioinformatics Py-module,
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 ... Keywords: struct-analysis
a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules. Keywords: struct-vis
(MOLecular PHYlogenetics) a computer program package for molecular phylogenetics. Keywords: bioinformatics
a protein structure analysis platform offering quality validation for 3D structures of proteins, nucleic acids and complexes. Keywords: struct-analysis,
one of the most popular programs for the generation of publication-quality figures. Keywords: struct-vis
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. Keywords: 2d-crystallograp,
(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences. Keywords: bioinformatics
a stand-alone program that calculates the accessible area of a molecule from a PDB format file. Keywords: struct-analysis sb,
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Keywords: sb,
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. Keywords: utilities
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). Keywords: bioinformatics
a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation. Keywords: struct-vis nucleic-acids,
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. Keywords: struct-analysis nucleic-acids,
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. Keywords: Py-module
a model building application for X-ray crystallography. Keywords: struct-vis,
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. Keywords: utilities
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. Keywords: struct-analysis
(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. Keywords: bioinformatics, sb,
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. Keywords: Py-module
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. Keywords: struct-analysis,
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. Keywords: utilities,
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 ... Keywords: struct-analysis, struct-vis,
a set of tools used by the PDB for processing and checking structure data. Keywords: struct-analysis, utilities,
(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. Keywords: tomography
(Pathologically Eclectic Rubbish Lister or sometimes called the Practical Extraction and Reporting Language) a highly capable, feature-rich family of programming languages. Keywords: utilities
a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. Keywords: utilities
(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Keywords: sb,
a free package of software programs for inferring phylogenies. Keywords: bioinformatics utilities,
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 ... Keywords: utilities
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 ... Keywords: utilities
(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. Keywords: utilities
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. Keywords: tomography,
a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers. Keywords: bioinformatics
an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools. Keywords: bioinformatics
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. Keywords: struct-analysis struct-vis,
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. Keywords: struct-analysis sb,
a protein structural dynamics analysis software package. ProDy is installed as a module within python. Keywords: Py-module,
the ultimate protein least squares fitting program. Keywords: struct-analysis sb,
(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. Keywords: struct-analysis bioinformatics,
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. Keywords: tomography
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). Keywords: struct-vis
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 ... Keywords: bioinformatics
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. Keywords: struct-vis
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. Keywords: bioinformatics Py-module,
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 ... Keywords: utilities
a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. Keywords: utilities,
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. Keywords: Py-module tomography,
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 ... Keywords: struct-analysis struct-vis,
detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules. Keywords: struct-analysis
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. Keywords: struct-analysis nucleic-acids,
a free software environment for statistical computing and graphics. Keywords: utilities
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. Keywords: struct-analysis nucleic-acids,
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. Keywords: struct-vis
a set of tools for generating high quality raster images of proteins or other molecules. Keywords: struct-vis
allows for semi-automated building of RNA structure within Coot. Keywords: nucleic-acids,
a fast, versatile and program for docking ligands to proteins and nucleic acids. Keywords: bioinformatics
(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. Keywords: sb,
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). Keywords: utilities,
(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. Keywords: struct-vis
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 ... Keywords: struct-analysis nucleic-acids,
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. Keywords: struct-analysis nucleic-acids,
a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. Keywords: sb,
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. Keywords: bioinformatics
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. Keywords: utilities
(Sequence Alignment and Modeling system) a collection of tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. Keywords: bioinformatics
(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. Keywords: bioinformatics ChIP-Seq, DNA-Seq, RNA-Seq,
a 2D image display and analysis program, specifically designed for single-particle EM. Keywords: 2d-crystallograp,
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 ...
Keywords: saxs
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. Keywords: saxs
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. Keywords: saxs
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. Keywords: saxs
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 ... Keywords: bioinformatics
(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 Keywords: Py-module
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. Keywords: saxs,
(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy. Keywords: sb,
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. Keywords: sb,
(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. Keywords: bioinformatics
a set of DNA sequence assembly, editing and analyzing tools. Developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK Keywords: bioinformatics
(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 ... Keywords: struct-analysis
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. Keywords: struct-analysis
a program that generates surfaces, density contours and gap regions from coordinate data supplied in a PDB file. Keywords: struct-analysis
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. Keywords: struct-analysis
an application that provides a user friendly interface allowing you to analyze several proteins at the same time. Keywords: struct-analysis struct-vis,
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). Keywords: bioinformatics
a program for the simultaneous superpositioning and analysis of multiple macromolecular structures via the method of maximum likelihood (ML). Keywords: struct-analysis
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. Keywords: utilities
a software package for comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments. Keywords: utilities
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 ... Keywords: utilities
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. Keywords: nucleic-acids
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 Keywords: struct-analysis,
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. Keywords: struct-vis
a slightly vectorized (AVX & SSE instructions) version of the original RELION 1.4 code by Dmitry Tegunov of the Max Planck Institute. Keywords: sb,
a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Keywords: struct-vis
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 ... Keywords: struct-analysis
searches PDB files for misidentified water molecules that should be modeled as cations. Keywords: struct-analysis,
command line tools for sequence logo generation. Keywords: bioinformatics
the protein verification tool from the WHAT IF program available as a free stand-alone program, complete with all source code. Keywords: struct-analysis sb,
a general protein analysis program. Keywords: struct-analysis
used for processing electron diffraction data. Previously available only on DEC Alpha. Keywords: 2d-crystallograp,
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. Keywords: utilities
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. Keywords: struct-vis,
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 ... Keywords: utilities