Jan 30 2023
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AlphaPickle
a multipurpose Python script for producing plots and user-legible files from the output of AlphaFold2 (notebook) and Colabfold (notebook).
Updated versions:
1.4.1 | Linux 64
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Jan 30 2023
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R-pkgs-SBGrid
contains optional R pkgs
Updated versions:
r3.5.1-latest | Linux 64
r3.5.1-20191216 | Linux 64
r3.5.1-latest | OS X INTEL
r3.5.1-20191216 | OS X INTEL
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Jan 26 2023
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POKY
a software suite for multidimensional NMR and 3D structure calculation of biomolecules.
Updated versions:
20220825 | Linux 64
20220825 | OS X INTEL
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Jan 26 2023
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MODELLER
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 and optimize various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.
Updated versions:
10.4 | Linux 64
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Jan 25 2023
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ChimeraX
the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.
Updated versions:
1.5_c8 | Linux 64
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Jan 25 2023
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NMRFx Structure
NMRFx Structure can be used to generate and analyze macromolecular structures and predict chemical shifts.
Updated versions:
11.1.37 | Linux 64
11.1.37 | OS X INTEL
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Jan 25 2023
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NMRFx Analyst
Software for NMR Processing, Visualization and Analysis
Integrates code of NMRFx Processor, Structure and additional tools
Updated versions:
11.3.0 | OS X INTEL
11.3.0 | Linux 64
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Jan 23 2023
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CCP-EM
(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.
Updated versions:
20221108 | Linux 64
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Jan 22 2023
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xds_relaytx
Updated versions:
20210205 | OS X INTEL
20210205 | Linux 64
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Jan 18 2023
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PDBstat
a C/C++ application developed as a coordinate and protein NMR restraint converter. This user-friendly tool provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, and analysis of atomic position consistency based on their convergence across a protein NMR ensemble.
Updated versions:
5.21.17 | Linux 64
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Jan 18 2023
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DENSS
(DENsity from Solution Scattering) an algorithm used for calculating ab initio electron density maps directly from solution scattering data.
Updated versions:
20221205 | Linux 64
20221205 | OS X INTEL
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Jan 15 2023
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MDAnalysis
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.
Updated versions:
2.4.2 | Linux 64
2.4.2 | OS X INTEL
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Jan 15 2023
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AlphaFold
an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions:
2.3.1 | Linux 64
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Jan 13 2023
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CCP-EM
(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.
Updated versions:
20221108 | OS X INTEL
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Jan 12 2023
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PyEM
Python modules and command-line utilities for electron microscopy of biological samples.
Updated versions:
20221207 | Linux 64
20221207 | OS X INTEL
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Jan 12 2023
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CcpNmr
a series of programs for macromolecular NMR spectroscopy integrated with 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).
Updated versions:
3.1.0 | Linux 64
3.1.0 | OS X INTEL
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Jan 09 2023
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DeepEMhancer
(Deep cryo-EM Map Enhancer) a python package designed to perform non-linear post-processing of cryo-EM maps for local sharpening, automatic masking and denoising. Systems using cuda 11+ should use the 20210511 version of deepEMhancer, and the modified models distributed in /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints/
Updated versions:
20200909 | Linux 64
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Jan 09 2023
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PHENIX
(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
Updated versions:
dev-4788 | Linux 64
dev-4788 | OS X INTEL
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Jan 09 2023
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R
a free software environment for statistical computing and graphics.
Updated versions:
4.2.1 | Linux 64
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Jan 09 2023
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NMR TITAN
is an easy-to-use software package for the two-dimensional lineshape analysis of titration experiments.
Updated versions:
1.6 | Linux 64
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Jan 07 2023
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Amber (DFCI only)
a suite of biomolecular simulation programs. The term "Amber" refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules (these force fields are in the public domain, and are used in a variety of simulation programs). Second, it is a package of molecular simulation programs which includes source code and demos.
Updated versions:
22 | Linux 64
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Jan 05 2023
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ChimeraX
the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.
Updated versions:
1.3_c8 | Linux 64
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Jan 05 2023
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AutoDock-GPU
AutoDock for GPUs and other accelerators, Cuda accelerated version of AutoDock4.2.6. It leverages its parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. The Cuda version was developed in collaboration with Nvidia to run AutoDock-GPU on the Oak Ridge National Laboratory's (ORNL) Summit, and it included a batched ligand pipeline developed by Aaron Scheinberg from Jubilee Development.
Updated versions:
1.5.3 | Linux 64
1.5.3 | OS X INTEL
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Jan 03 2023
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RNA Framework
a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data. Toolkit will help with automatic reference transcriptome creation, automatic reads preprocessing (adapter clipping and trimming) and mapping, scoring and data normalization, and accurate RNA folding prediction by incorporating structural probing data.
Updated versions:
8596c2e | Linux 64
8596c2e | OS X INTEL
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Jan 03 2023
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AmberTools
a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.
Updated versions:
22 | Linux 64
22 | OS X INTEL
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