Protein Interaction

The Genome Positioning System (GPS) is a software tool to study protein-DNA interaction using ChIP-Seq data. GPS builds a probabilistic mixture model to predict the most likely positions of binding events at single-base resolution. GPS is a Java software, so it runs on multiple platforms,... Platforms: Windows

Bio::Network::IO::dip_tab is a Perl class for parsing interaction data in DIP tab-delimited format. SYNOPSIS Do not use this module directly, use Bio::Network::IO. For example: my $io = Bio::Network::IO->new(-format => dip_tab, -file => data.dip); my $network = $io->next_network; The... Platforms: *nix

To further understand the implementation of hyperparameters re-estimation technique in Bayesian hierarchical model, we added two more prior assumptions over the weight in BayesPI, namely Laplace prior and Cauchy prior, by using the evidence approximation method. In addition, we divided... Platforms: Matlab

This contest concerns a very simplified two-dimensional version of the protein folding problem. Given the amino acid sequence of a simplified protein, your job is to determine a final "optimally folded" configuration. Each potential arrangement of the protein sequence is associated with an energy... Platforms: Matlab

HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures. Features . Protein Structure Quality... Platforms: *nix

CLC Protein Workbench is a scientific application for bioinformation, aimed at the advanced analysis of protein sequences. This program offers you a really wide range of analyses, all of them integrated in the same interface, which is very friendly and accessible to all users.The options and... Platforms: Windows

Protein BLAST Widget provides a quick access to the Protein Basic Local Alignment Search Tool at NCBI. You just have to type or paste your sequence and to select the program to be used. Platforms: Mac

Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of... Platforms: Windows, Mac, Linux

GRaPe - a platform-independent software tool for building integrative gene-reaction-protein (GRP) networks. It generates the kinetic equations for each reaction and outputs a SBML document. It also implements two methods for parameter estimation. Platforms: Windows, Mac, Linux

User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files Platforms: Windows, Mac, Linux

The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs. Platforms: Windows, Mac, Linux

Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files Platforms: Windows, Mac, Linux

The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. Platforms: Windows, Mac, BSD, Linux

The sixth MATLAB Programming Contest, Protein, will run from November 6-13, 2002.This contest concerns a very simplified two-dimensional version of the protein folding problem. Given the amino acid sequence of a simplified protein, your job is to determine a final "optimally folded"... Platforms: Matlab

Allows the user to calculate her optimum post-workout protein shake recipe and determine right mixture of these three essential ingredients, plus her daily recommended protein dose: 1. Protein 2. Carbohydrate 3. WaterAll calculations are based on her body weight. Install : 1. Unzip the... Platforms: PHP

Allows user interaction among a trusted community of users to foster a more direct and personal exchange of ideas.This module was created for a specific project of EKOS Communications. The intention of the module was to foster communication between users of a private website. The users and... Platforms: PHP

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =... Platforms: *nix

Brcontrol is a set of patches to allow some interaction between a IDS and a firewall (currently snort and linux netfilter). It will help in the creation of aggresive honeypots or other advanced firewall and ids configurations. In can also work as bridge.. Get Brcontrol at SourceForge.net. Fast,... Platforms: *nix

grammydotru123 eases interaction with the MP3 portal grammy.ru. It works in this way: you seek up the url of an artist or an album at grammy.ru, and then just invoke grammydotru123 or python grammydotru123 and it fetches all songs belonging to the artist/album (a song of an album of... Platforms: *nix

Etiquette provides an interaction protocol construction tool. Etiquette is an interaction protocol construction toolkit. The projects goal is to build a framework for rapid design of network communication code. Etiquette interaction protocols are intended to describe valid communication... Platforms: *nix