Muscle Milk Protein Shakes

Software to cluster protein sequences into functionally similar groups. Journal reference: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/16/1765 Platforms: Mac, Linux

Real time facial animation package based on muscle model of the face. Includes basic scripting language, full API, animation compositing, tools for creating and exporting muscles in 3D studio max. Platforms: Windows, Mac, Linux

gbwget is a command line/screen oriented tool to search in nucleotideor protein databases and to view or retrieve database entries. It can easily integrated into the EMBOSS seqence analysis Suite can also be used standalone. Platforms: Windows, Mac, Linux

FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences. Platforms: Mac, BSD, Linux

ICRPfinder finds or generates DNA patterns which can include restriction enzyme recognition sites in coding sequences without changing the translated protein sequence. Platforms: Windows, Mac, Linux

Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Platforms: Windows, Mac, Linux

JNutrition is a Nutrition Manager. Create meal plans and let it calculate the calories, carbs, protein and fat of it. It is still not finish, but most functions work. Platforms: Mac

The JPAT API is a Java API designed to provide developers with tools for calculating the results of protease digestion of proteins and ms/ms fragmentation of peptides. JPAT also contains GUI components for displaying the results. JPAT is a nice way to get Platforms: Windows, Mac, Linux

NOC is a open source development toolkit and a powerful molecular explorer for protein structure visualizing,analysis,crystallographic mapping, modeling, and refinement, Gromacs/Amber MD trajectories displaying,movie making... Platforms: Windows, Mac, BSD, Linux

Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments. Platforms: Windows, Mac, Linux

An open source implementation of a protein threading program based on the energy functions and techniques originally introduced by Prospect. Platforms: Mac, BSD, Linux

ProteinShop is an interactive protein manipulation tool. Users apply their knowledge and intuition to quickly create a set of protein configurations that can be subjected to local or global optimization. More information at http://proteinshop.org Platforms: Mac, BSD, Linux

A web based application to track protein related reagents including DNA constructs, cell lines, supes, and purified proteins. Supports creating, tracking, and prioritizing requests for transfections and DNA. Includes search and PDF reports. Platforms: Windows, Mac, Linux

PANTHER project: software for modeling of protein sequence and function evolution, and tools for applying these data to the analysis of genome data, expression data and coding SNPs. Details available at http://www.pantherdb.org. Platforms: Windows, Mac, Linux

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. Platforms: Windows, Mac, Linux

This Java software implements Profile Hidden Markov Models (PHMMs) for protein classification for the WEKA workbench. Standard PHMMs and newly introduced binary PHMMs are used. In addition the software allows propositionalisation of PHMMs. Platforms: Windows, Mac, Linux

PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP. Platforms: Windows, Mac, Linux

A tool to compare two Protein Sequences and show similarities with the help of dotplot. Platforms: Windows, Mac, Linux

Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics. Platforms: Windows, Mac, Linux

A library and associated applications for searching for patterns in protein structures and measuring geometric parameters. Platforms: Windows, Mac, Linux