May 31 2018
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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:
2.4.10 | OS X INTEL
2.4.10 | Linux 64
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May 29 2018
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STAMP
(STructural Alignment of Multiple Proteins) a suite of programs to compare and align protein 3-D structures. It will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. It will also search a database of protein structures to identify structurally similar proteins and includes a number of utility programs for the manipulation of protein structures.
Updated versions:
4.4.2 | OS X INTEL
4.4.2 | Linux 64
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May 29 2018
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XDSSTAT
a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.
Updated versions:
20180223 | Linux 64
20171011 | OS X INTEL
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May 29 2018
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XDSGUI
a GUI (graphical user interface) for XDS designed to help both novice and experienced users; it enables XDS data processing without the command line and supplies additional graphical information in a simple, user-modifiable and user-extensible way. It graphically displays the ASCII and cbf files that XDS writes and can run useful shell commands with a simple mouse click.
Updated versions:
20180427 | OS X INTEL
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May 29 2018
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vmd-xplor
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.
Updated versions:
1.9.1a | OS X INTEL
1.9.1a | Linux 64
1.11 | OS X INTEL
1.11 | Linux 64
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May 29 2018
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Staden
a set of DNA sequence assembly, editing and analyzing tools developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
Updated versions:
2.0.0b11 | Linux 64
2.0.0b11 | OS X INTEL
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May 29 2018
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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:
2.5 | Linux 64
2.5 | OS X INTEL
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May 29 2018
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ProDy
a protein structural dynamics analysis software package.
ProDy is installed as a module within python.
Updated versions:
1.9.4 | Linux 64
1.8.2 | OS X INTEL
1.10.7 | OS X INTEL
1.9.4 | OS X INTEL
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May 29 2018
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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:
7.2.1 | Linux 64
7.2.1 | OS X INTEL
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May 29 2018
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NMRPipe
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.
Updated versions:
20180523 | Linux 64
20180523 | OS X INTEL
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May 29 2018
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MOSFLM
a package for processing film and image plate data.
Updated versions:
7.2.2 | Linux 64
7.2.2 | OS X INTEL
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May 29 2018
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iMosflm
a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package.
Updated versions:
7.2.2 | Linux 64
7.2.2 | OS X INTEL
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May 23 2018
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gmconvert
converts both a 3D density map and an atom model into GMM (gaussian mixture model) by employing an EM (expectation maximization) algorithm. The program also has many other useful functions to handle GMM.
Updated versions:
20180516 | Linux 64
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May 23 2018
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gmfit
superimposes molecular subunits into the density map of their complex. To reduce computational costs for the superimposing, both subunits and complexes are transformed into GMM (Gaussian Mixture Model) using the gmconvert program. Although designed to superimpose multiple atomic models of subunits into a low-resolution 3D density map, gmfit can also be applied to superimposing two 3D density maps or two atomic models.
Updated versions:
20180516 | Linux 64
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May 14 2018
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CellProfiler
is a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
Updated versions:
3.1.3 | Linux 64
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