Jan 31 2021
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SBGrid Installer
a graphical installation client used to install the SBGrid software collection on Apple OSX computers running MacOSX v10.13 - 10.15. Users can cherrypick a subset of applications for installation on their laptops or desktops. Software updates are highlighted, but users trigger the software update manually at their convenience.
Updated versions:
2.1.4 | Linux 64
2.1.4 | OS X INTEL
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Jan 29 2021
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CTFFIND 4
a new version of ctffind (a program for finding CTFs of electron micrographs) that should run significantly faster than CTFFIND 3 and may give slightly improved results when processing data from detectors other than scanned photographic film.
Updated versions:
4.1.14-c7 | Linux 64
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Jan 29 2021
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SIMPLE
(Single-particle IMage Processing Linux Engine) does ab initio 3D reconstruction (programs cluster & origami), heterogeneity analysis (programs cluster, origami & cycler), and high-resolution refinement (programs align, reconstruct, automask & cycler).
Updated versions:
3.0 | OS X INTEL
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Jan 28 2021
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Python
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 in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.
Updated versions:
3.6.5 | Linux 64
3.6.5 | OS X INTEL
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Jan 28 2021
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Google Cloud SDK
tools and libraries for interacting with Google Cloud products and services.
Updated versions:
316.0.0 | OS X INTEL
316.0.0 | Linux 64
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Jan 26 2021
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CAVER Analyst
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.
Updated versions:
2.0-beta | OS X INTEL
2.0-beta | Linux 64
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Jan 25 2021
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schrodinger_suite
A Schrodinger installation that does not include the SBGrid license, otherwise same as schrodinger.
Updated versions:
2020-2 | Linux 64
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Jan 25 2021
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PEET
(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.
Updated versions:
1.15.0 | OS X INTEL
1.15.0 | Linux 64
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Jan 25 2021
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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:
1.19.1-4122 | Linux 64
1.19.1-4122 | OS X INTEL
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Jan 22 2021
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MAFFT
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).
Updated versions:
7.475 | Linux 64
7.475 | OS X INTEL
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Jan 22 2021
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nmrglue
a python module for reading, writing, and interacting with the spectral data stored in a number of common NMR data formats.
Updated versions:
0.7 | OS X INTEL
0.7 | Linux 64
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Jan 21 2021
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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:
3.0.3 | Linux 64
3.0.3 | OS X INTEL
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Jan 21 2021
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CCP4
(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.
Updated versions:
7.1.010 | Linux 64
7.1.010 | OS X INTEL
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Jan 21 2021
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LightDock
a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm.
Updated versions:
0.8.1 | OS X INTEL
0.8.1 | Linux 64
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Jan 20 2021
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Julia
The Julia programming language is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
Updated versions:
1.4.2 | Linux 64
1.3.1 | Linux 64
1.4.2 | OS X INTEL
1.3.1 | OS X INTEL
1.5.3 | Linux 64
1.5.3 | OS X INTEL
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Jan 20 2021
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schrodinger_suite
A Schrodinger installation that does not include the SBGrid license, otherwise same as schrodinger.
Updated versions:
2020-3 | Linux 64
2020-4 | Linux 64
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Jan 19 2021
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IGV
(Integrative Genomics Viewer) 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.
Updated versions:
2.8.13 | Linux 64
2.8.13 | OS X INTEL
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Jan 13 2021
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ChimeraX
a next-generation molecular visualization program, 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. ChimeraX will have documented programming interfaces and an easy-to-use “Tool Shed” web repository of extensions.
Updated versions:
1.1.1 | Linux 64
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Jan 13 2021
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SBGrid Installer
a graphical installation client used to install the SBGrid software collection on Apple OSX computers running MacOSX v10.13 - 10.15. Users can cherrypick a subset of applications for installation on their laptops or desktops. Software updates are highlighted, but users trigger the software update manually at their convenience.
Updated versions:
2.1.3 | Linux 64
2.1.3 | OS X INTEL
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Jan 12 2021
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CHAP
(The Channel Annotation Package) a tool for the functional annotation of novel ion channel structures that provides information on the biophysical properties of the ion permeation pathway by utilising molecular dynamics simulations.
Updated versions:
0.8.0 | OS X INTEL
0.9.1 | OS X INTEL
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Jan 08 2021
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LigPlot+
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.
Updated versions:
2.2 | OS X INTEL
2.2 | Linux 64
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Jan 08 2021
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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:
3.3.0 | Linux 64
3.3.0 | OS X INTEL
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Jan 04 2021
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TVIPS tools
for the conversion of microED data collected on TVIPS TemCam-F416, Thermo Fisher CetaD, and Thermo Fisher Falcon III to SMV crystallographic format (*.img)
Updated versions:
20201231 | Linux 64
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