Jun 29 2023
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LigPlot+
the successor to the original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.
Updated versions:
2.2.8 | OS X INTEL
2.2.8 | Linux 64
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Jun 29 2023
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Coot
(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.
Updated versions:
0.9.8.8 | OS X INTEL
0.9.6 | OS X INTEL
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Jun 28 2023
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cs2star
A simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.
Updated versions:
0.5.4 | OS X INTEL
0.5.4 | Linux 64
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Jun 28 2023
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POKY
a software suite for multidimensional NMR and 3D structure calculation of biomolecules.
Updated versions:
20230511 | OS X INTEL
20230511 | Linux 64
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Jun 27 2023
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BUSTER
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.
Updated versions:
20230614 | OS X INTEL
20230614 | Linux 64
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Jun 26 2023
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AlphaPulldown
a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.
Updated versions:
0.30.7 | Linux 64
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Jun 25 2023
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EMReady
improves the quality and interpretability of cryo-EM maps by local and non-local deep learning
Updated versions:
20230606 | Linux 64
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Jun 23 2023
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imod2relion
A tool reading IMOD points, obtaining particles' info and generating .star file for RELION.
Updated versions:
1.1.0 | OS X INTEL
1.1.0 | Linux 64
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Jun 20 2023
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HKL2MAP
a graphical user-interface for macromolecular phasing.
Updated versions:
0.4.e-beta | OS X INTEL
0.4.e-beta | Linux 64
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Jun 20 2023
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RNAstructure
a complete package for RNA and DNA secondary structure prediction and analysis.
Updated versions:
6.4 | Linux 64
6.4 | OS X INTEL
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Jun 18 2023
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DiffDock
a state-of-the-art method for molecular docking
Updated versions:
73ef67f | Linux 64
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Jun 15 2023
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deltaVina
is a scoring function for rescoring protein-ligand binding affinity
Updated versions:
20230614 | Linux 64
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Jun 15 2023
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deltaVinaXGB
is a machine-learning based protein-ligand scoring function.
Updated versions:
20230614 | Linux 64
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Jun 15 2023
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deepTools
a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
Updated versions:
3.5.2 | Linux 64
3.5.2 | OS X INTEL
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Jun 15 2023
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MMseqs2
an ultra fast and sensitive sequence search and clustering suite
Updated versions:
14.7e284 | OS X INTEL
14-7e284 | Linux 64
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Jun 14 2023
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DiffDock
a state-of-the-art method for molecular docking
Updated versions:
3d45728 | Linux 64
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Jun 13 2023
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Topaz
a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.
Updated versions:
0.2.5a | Linux 64
0.2.5_cu11.2 | Linux 64
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Jun 13 2023
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Xplor-NIH
a package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was derived from XPLOR version 3.851 and contains all of the functionality therein in addition to numerous new features designed to render a highly flexible architecture and foster the rapid and easy development of new functionality.
Updated versions:
3.7 | Linux 64
3.7-arm | OS X INTEL
3.7 | OS X INTEL
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Jun 12 2023
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ShapeMapper2
a completely rewritten version of our ShapeMapper for reading out the results of an RNA chemical probing experiment by massively parallel sequencing that integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to identify RNA adduct sites.
Updated versions:
2.2 | Linux 64
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Jun 12 2023
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Julia
is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
Updated versions:
1.9.1 | Linux 64
1.9.1 | OS X INTEL
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Jun 12 2023
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DIALS
(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.
Updated versions:
3.14.2 | OS X INTEL
3.13.0 | OS X INTEL
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Jun 12 2023
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IMOD
a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
Updated versions:
4.12.47 | Linux 64
4.11.24 | Linux 64
4.12.47 | OS X INTEL
4.11.24 | OS X INTEL
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Jun 12 2023
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DIALS
(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.
Updated versions:
3.14.2 | Linux 64
3.13.0 | Linux 64
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Jun 12 2023
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BioXTAS RAW
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.
Updated versions:
2.2.0 | Linux 64
2.2.0 | OS X INTEL
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Jun 12 2023
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OpenMM
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.
Updated versions:
8.0.0 | Linux 64
7.7.0 | Linux 64
8.0.0 | OS X INTEL
7.7.0 | OS X INTEL
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Jun 11 2023
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PyMOL
widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.
Updated versions:
2.5.4_420 | OS X INTEL
2.4.1_228 | OS X INTEL
2.2.3 | OS X INTEL
2.5.4_404 | Linux 64
2.4.1_198 | Linux 64
2.2.3 | Linux 64
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Jun 09 2023
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Careless
merges crystallography data without much physics. It performs scaling, merging, and French-Wilson corrections in a single step by directly inferring structure factor amplitudes from unscaled, unmerged intensities.
Updated versions:
0.3.0 | Linux 64
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