Software Updates

IGV

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.

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.

ProDy

a protein structural dynamics analysis software package.

ProDy is installed as a module within python.

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.

XDSSTAT

a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.

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.

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.

Staden

a set of DNA sequence assembly, editing and analyzing tools developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

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).

ProDy

a protein structural dynamics analysis software package.

ProDy is installed as a module within python.

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.

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.

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.

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.

MOSFLM

a package for processing film and image plate data.

iMosflm

a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package.

Geneious

a powerful and comprehensive suite of molecular biology and NGS analysis tools.

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.

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.

SBGrid Installer

a graphical installation client used to install the SBGrid software collection on Apple OSX computers running MacOSX v10.9 - 10.12. 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.

Chimera

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.

CellProfiler

designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

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.

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.