Protein Hydrolysis

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.

Several RNA and protein structure volume calculation tools.

The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.


Platforms: Windows, Mac, Linux

BioQuery is a bioinformatics tool that acts as a query builder for genetic, protein, publication, and other biomedical databases. BioQuery is also an update service that periodically resubmits saved searches and sends you new data as it is found.


Platforms: Windows, Mac, Linux

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


Platforms: 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