Projects

GNAT NER

GNAT is a library and web service capable of performing gene entity NER and normalization of biomedical articles. Mentions of genes and proteins in the articles are linked to to Entrez Gene identifiers. GNAT is available both for local download (suitable for large-scale processing) and as a web ... [More] service (suitable for more limited processing or testing). A combination of local and remote processing is also available, where CPU-heavy operations are performed locally and memory-intensive operations are performed remotely (this is suitable for large-scale processing where a large amount of memory is not available). GNAT uses LINNAEUS (Gerner et al., 2010) for species detection and BANNER (Leaman et al., 2008) in one part of its false positive filtering process. [Less]

relax (molecular dynamics analysis)

relax is a program designed for the study study of molecular dynamics of organic molecules, proteins, RNA, DNA, sugars, and other biomolecules through the analysis of experimental NMR data. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of ... [More] the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model or ensemble analysis and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, and the investigation of stereochemistry. [Less]

Python Macromolecular Library (mmLib)

The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and provides ... [More] a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer. The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization. [Less]

mmdb

MMDB is a macromolecular coordinate library, written by Eugene Krissinel. It supports reading and writing two file formats, PDB and mmCIF, and provides high-level tools for working with coordinate files: orthogonal-fractional coordinate transforms, generation of symmetry mates, editing the ... [More] molecular structure and some others. Tarballs available at: ftp://ftp.ccp4.ac.uk/opensource/ [Less]

Force Field X

Force Field X is a group of open source (GPL v. 3), platform independent (Java Runtime Environment) modules for molecular biophysics. Key methods include: 1) Polarizable AMOEBA force fields 2) Particle-mesh Ewald electrostatics 3) Generalized Kirkwood continuum electrostatics ... [More] 4) X-ray and neutron crystallography refinement 5) Real space refinement for CryoEM 6) Methods for structure based drug design [Less]

PPI Benchmark

A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.

iligner

This is a project to develop the next generation of sequence alignment editor for the Mac OS X platform. It is being developed in the Cocoa framework to produce a fast and intuitive tool for manual and semi-automated sequence alignment.

sire

SireMolecular modelling package in early developmental stageSire has been in development for 4 years, and has had a small technology preview release. An alpha version of the code was used to run the QM/MM Monte Carlo simulations that are published in the Journal of Chemical Physics ... [More] (http://link.aip.org/link/?JCP/128/014109). Development of Sire is slow and steady - although Sire is now generally usable. If you are interested in taking a look and playing with a molecular simulation program that is totally different to the rest, then see http://siremol.org If you want a more up-to-date description of progress, and to find out the ideas that underly the development of Sire, then please read the blog, http://siremol.org/blog Alternatively. you can follow the day-to-day development by checking out my subversion commit log (http://groups.google.com/group/sire-svn) [Less]

charmming

What is CHARMMingCHARMMING is a public domain web portal to the CHARMM molecular simulation program, which must be licensed separately. It includes functionality for uploading structures, visualizing them, and performing minimization, solvation, and classical molecular dynamics. MPORTANT ... [More] NOTEAlthough you can set up CHARMMing for your own research group, CHARMM's license prohibits you from making it available to anyone who does not have a license. You are responsible for ensuring that access to your CHARMMing server is limited only to those people who are part of a research group that possesses a CHARMM license. Getting CHARMMingYou can find released versions of CHARMMing on the project's download page. The latest released version is 0.5.1. You can also get the latest released installer version from Subversion with svn co http://charmming.googlecode.com/svn/installer/INSTALLER_0_5 . DocumentationComplete install documentation Change log for version 0.5 Quick start guide [Less]

gendi

GENDI is now called EPIDI (Epitope Discovery Indexer) EPIDI is a Eclipse based robot software for search in genetic prediction sites like: EpiJen (http://www.jenner.ac.uk/EpiJen/) RankPEP (http://immunax.dfci.harvard.edu/Tools/rankpep.html) ProPred (http://www.imtech.res.in/raghava/propred/) ... [More] SYFPEITHI (http://www.syfpeithi.de/Scripts/MHCServer.dll/EpitopePrediction.htm) HLA Peptide Binding Predictions (http://www-bimas.cit.nih.gov/molbio/hla_bind/) RankPEP (http://bio.dfci.harvard.edu/RANKPEP/) Releases soon for windows, linux and mac osx [Less]