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Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.
The Simple Semantic Classifier classifies short chunks of natural language text into broad semantic classes that correspond to the OBO ontologies provided as input.
Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.
This is a set of scripts that helps with processing of NMR pH titration data. These scripts allow for fitting (using R) and plotting of data of multiple residues. The program needs to be made more user friendly.
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BLOSpectrum tools provide programs to automatically classify proteins according to SCOP database. In order to achieve such a goal, they implements all the required information theory widgets on BLOSpectrum fingerprints.
Cscape is an application for visualizing and navigating through data from a Reverse Phase Protein Microarray (RPMA). Cscape uses the Google Maps API to map the RPMA data on top of an image of a cancer cell and its associated pathways.
SDFCherry is a command-line program that searches for textual matches in molecular structure files of SDF format and outputs the structures that match. Optionally adds a data field to the matched structures, e.g., biological activity. Useful for QSAR.
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A family of programs for building coarse-grained models (eg. of macromolecules), manipulating them (geometrical transformations and more) and calculating their X-ray scattering patterns (1D and 2D too). Uses PVM for parallelization.
Contains various algorithms that maps short reads produced from Illumina (Solexa) Genome Analyzer, or Applied Biosystems' SOLiD System, to a reference sequence or a set of reference sequences.
Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.
Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.
Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.
This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).
ChIPOTle 2.0 is a user friendly tool for performing peak detection in ChIP-chip signal. The tool also has functions for probe sorting, signal normalization, replication merging, and multiple correction testing in a windows interface or *nix commandline.
GLARE is a library and a software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.
NullAllEst is the implementation of a maximum likelihood algorithm to estimate the frequency of a null allele in microsatellite genetic data. A Markov Chain Monte Carlo simulation is used to solve the likelihood function.