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