Software Updates

Namdinator

a commandline tool, written in BASH, that sets up and runs a MDFF (molecular Dynamics Flexible Fit) simulation in a semi automatic manner, using only the input PDB file and input density file.

HKL2000

a data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection strategy and processing data. HKL is based on the extended versions of Denzo, Xdisplayf and Scalepack. HKL was developed and is maintained by Wladek Minor (University of Virginia).

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.

Neggia

an HDF5 read plugin for XDS. Neggia presents HDF5 data to XDS in a fully parallelized way, directly and without interconversion and speeds up the processing of HDF5 data.

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.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

GROMACS

a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.

DivCon Discovery Suite

implements fast, high-performance, quantum mechanical and molecular mechanical algorithms in an easy-to-use approach to accelerate drug discovery and development.

FFmpeg

a complete, cross-platform solution to record, convert and stream audio and video.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Rosetta

a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

BLAST+

a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.

EMAN2

a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications.

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.

Surface Racer

calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside.

HKL2000

a data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection strategy and processing data. HKL is based on the extended versions of Denzo, Xdisplayf and Scalepack. HKL was developed and is maintained by Wladek Minor (University of Virginia).

GROMACS

a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.