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SBGridTV

Supported Applications

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Name Description Links
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.
Keywords:
Utilities
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.

Restriction: available to nonprofit users who register using the htmd_register command.

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.
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:
Genomics
a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.
a "pipeline" for processing and analysis of EM images. 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 using tightly integrated SQL databases.
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,
a 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.
Keywords:
NMR
an interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.

Restriction: available to nonprofit users who register and download ARP/wARP individually. See detailed instructions.

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.

Restriction: available to nonprofit users who register with EMBL & submit confirmation to SBGrid.

Keywords:
SAXS
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.

Restriction: available to non-profit users who register with Global Phasing and copy license file to /programs/local/autoproc/autoproc_licence.

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

Restriction: available to nonprofit users who register with EMBL & submit confirmation to SBGrid.

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.
Keywords:
Utilities
a set of command line tools written in C and making use of the BiopLib library for manipulation of protein structure and sequence.
a set of tools for biological computation written in Python by an international team of developers.
Keywords:
Utilities
a program for analysis of SAXS data that 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.
Keywords:
SAXS
(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.
an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
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.

Restriction: available to nonprofit users who register with Global Phasing and copy license file to /programs/local/buster/buster_licence.

(Computer Aided Resonance Assignment) an application for the analysis of NMR spectra and computer-aided resonance assignment.
Keywords:
NMR
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.
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).
Keywords:
NMR
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.
Keywords:
NMR
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 next-generation molecular visualization program, following UCSF Chimera. Compared to Chimera, ChimeraX has better graphics (e.g., interactive ambient shadows), handles large structures (millions of atoms) much faster, and has a more modern, single-window user interface. ChimeraX will have documented programming interfaces and an easy-to-use “Tool Shed” web repository of extensions.
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 quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods, and classical force fields.
a program for non-linear least squares fitting of CPMG relaxation dispersion curves.
Keywords:
NMR
a program for cutting sections out of 2D and 3D density maps.
crossflaghkl partitions a merged hkl-file into k subsets with the number of reflections marked with -1.
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.
Keywords:
NMR
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.
Redistributable software libraries to support CUDA applications for Linux.
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.

Restriction: available to users with an active CYANA software license.

Keywords:
NMR
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:
Python Module
a program for calculating protein electrostatics.

Restriction: available to nonprofit users who register with Columbia & submit confirmation to SBGrid.

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.
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. Dock is offered in the SBGrid collection in ...
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 hydrophilicity in terms of the energy of interaction of a water molecule with the surrounding atoms. Experience has shown that cavities with interaction energies below -12 kcal/mol tend to be filled, and cavities for which the energy is above that threshold, tend to be empty.
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.
(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.

Restriction: available to users with an activate d*TREK software license.

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.
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.
a simple program that converts diffraction images from EIGER in the HDF5 format to the miniCBF format.
(ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography.
Keywords:
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.
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.
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).
integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
Keywords:
Utilities
(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 and classifies these interactions into hydrogen bonds, electrostatic, hydrophobic, and Van der Waals. Entangle also recognizes when a stacking interaction occurs between two aromatic residues.
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.

Restriction: available to nonprofit users who register with EMBL & submit confirmation to SBGrid.

(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.
Keywords:
NMR
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
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.
determines the detective quantum efficiency (DQE) of a detector.
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.
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.
Keywords:
NMR
(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.
Keywords:
NMR
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.

Restriction: 13-seat floating license available to non-profit groups.

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.
Keywords:
Utilities
combined installation of autoPROC, BUSTER, and SHARP available to Global Phasing consortium members.

Restriction: available to Global Phasing Consortium members with an active license.

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
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.
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.
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).

Restriction: must obtain software license from developer & copy license file to /usr/local/lib.

a graphical user-interface for macromolecular phasing.

Available to nonprofit users who register with EMBL & submit confirmation to SBGrid.

a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels.
a program intended for the calculation of NMR relaxation of small, quasirigid macromolecules whose structure, with atomic resolution, is taken from a PDB file of atomic coordinates. HYDRONMR evaluates basic hydrodynamic quantities involved in dynamic NMR in the same fashion as HYDROPRO program, then calculates NMR quantities (T1, T2, NOE, etc) for each residue of a globular protein and reports the translational diffusion coefficient ...
Keywords:
NMR
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.
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 that includes the original IHRSR functionality but can also determine out-of-plane tilt, apply dihedral symmetry, and automatically construct a starting model from the image data Perl and Spider scripts allow users to perform common tasks: power spectra calculations, CTF corrections, image stack generation, image centering, and tube diameter determination.
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 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.
a software suite to create, edit, compose, or convert bitmap images.
Keywords:
Utilities
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.
(INFERence of RNA ALignment) searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
Keywords:
Genomics
(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk.
Keywords:
2DX
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.
Keywords:
Python Module
an algorithm to reconstruct non-uniformly acquired NMR data.
Keywords:
NMR
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: *
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.
Keywords:
Bioimaging
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 describe the direction and magnitude of a bend angle for analysis of DNA and DNA/protein complex geometries.
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.
an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
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.
Keywords:
SAXS
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.
a series of software tools for docking flexible ligands into receptors with selective flexibility, comprising: 1) AutoDockFR: a docking engine using the AutoDock4 forcefield; 2) AutoGridFR: a graphical user interface for setting up docking boxes; 3) AutoSite: a ligand binding site detection and characterization program.
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.
Keywords:
Python Module
(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.
Keywords:
NMR
used for homology or comparative modeling of protein three-dimensional structures. From a sequence alignment with known related structures MODELLER automatically calculates a model containing all non-hydrogen atoms using comparative protein structure modeling by satisfaction of spatial restraints. It can also perform de novo modeling of loops in protein structures, optimize various models of protein structure with respect to a flexibly defined objective function, multiple ...
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.
Keywords:
NMR
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.
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.
an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
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.
a program that corrects whole frame image motion recorded with dose fractionated image stacks.
a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
Keywords:
Utilities
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.
Keywords:
Utilities
an HDF5 read plugin for XDS. NEGGIA presents HDF5 data to XDS in a fully parallelized way, directly and without interconversion and speeds up the processing of HDF5 data.
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.
Keywords:
NMR
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).
is a new version of Sparky renamed because NMRFAM has taken over the original Sparky to support advances in the biomolecular NMR field. Tom Ferrin and Tom Goddard of UCSF, generously allowed NMRFAM to develop this the original Sparky, which remains the most popular NMR biomolecular analysis tool available.
Keywords:
NMR
Software for Processing Multi-Dimensional NMR Spectra featuring quality, and performance to handle complex data analyses.
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.
Keywords:
NMR
used to visualize and Analyze Nuclear Magnetic Resonance Data.
Keywords:
NMR
Visualize and Analyze Nuclear Magnetic Resonance Data.
Keywords:
NMR
a software suite for the modelling of large conformational changes of 3-D protein structures under the constraint of a low resolution electron density map. Norma is used to interpret electron microscopy data using atomic scale resolution structural models and perform flexible fitting on new cases without encountering major technical difficulties.
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.
Keywords:
Python Module
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.
Keywords:
Utilities
(Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE).