Protein Similarity

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

MarcXimiL is a flexible multi-platform bibliographic similarity analysis framework. Features: deduplication, information monitoring, visual analysis, plagiarism detection. Supported: MARCXML, OAI-PMH2 harvesting, and importation of text MARC. Platforms: Windows, Mac, BSD, Solaris, Linux

A similarity-free approach to compare the diversity of environmental viral communities 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

Prodar is a search application that queries the PDB for candidate structural alignments. The input to the search is a protein backbone structure read from a standard (text) PDB file, and the results returned are based solely on structural similarity of the backbone without any regard to sequence... Platforms: Windows, Mac

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

ngram is a module to compute the similarity between two strings. It is different to python's 'difflib.SequenceMatcher' in that it cares more about the size of both strings. ngram is an port and extension of the perl module called 'String::Trigram Platforms: Windows, Mac, Linux

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

SIM-DL: Semantic Similarity Measurement Server for concepts (and individuals) represented using (expressive) Description Logics (DL). 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

The Swiss Protein Identification Toolbox (swissPIT) is a project at the Swiss Institute for Bioinformatics (SIB) in Geneva which aims at the development of an automated analysis system to identify proteins using MS and MS/MS based data. Platforms: Windows, Mac, Linux

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