Protein Hydrolysis
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
License: Freeware | Size: 9.89 MB | Download (43): IMPACT Download |
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
License: Freeware | Size: 2.59 MB | Download (46): JNutrition Download |
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
License: Freeware | Size: 190.09 KB | Download (43): JPAT - Java Protein Analysis Tools Download |
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
License: Freeware | Size: 5.75 MB | Download (43): NOCH Download |
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
License: Freeware | Size: 7.52 MB | Download (45): Open2Dprot Download |
An open source implementation of a protein threading program based on the energy functions and techniques originally introduced by Prospect.
Platforms: Mac, BSD, Linux
License: Freeware | Size: 173.57 MB | Download (44): OpenProspect Download |
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
License: Freeware | Size: 6.73 MB | Download (44): ProteinShop Download |
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
License: Freeware | Size: 10.88 MB | Download (47): ProteinTracker Download |
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
License: Freeware | Size: 22.4 MB | Download (44): PANTHER Download |
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
License: Freeware | Size: 6.47 MB | Download (48): PDB2PQR Download |
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
License: Freeware | Size: 6.43 MB | Download (43): pHMM4weka Download |
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
License: Freeware | Size: 98.61 KB | Download (44): PSIsoft - The PSIMAP Software Project Download |
A tool to compare two Protein Sequences and show similarities with the help of dotplot.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 49.6 KB | Download (43): Sequence Alignment Download |
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
License: Freeware | Size: 12.66 MB | Download (44): StrBio java class libraries Download |
A library and associated applications for searching for patterns in protein structures and measuring geometric parameters.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 112.21 KB | Download (45): Tailor Download |
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
License: Freeware | Size: 9.48 MB | Download (44): swissPIT Download |
NCBI has an implementation of BLAST algorithm on their website at www.ncbi.nlm.nih.gov/BLAST, which is good if you want to query short DNA or protein sequence against various sequence databases. The problem arises when large sequences need to be BLAST'ed against a sequence database or against...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (40): GUI for Basic Local Alignment Search Tool (BLAST) Download |
The FindCore Toolbox (v. 1.0b)David Snyder and Gaetano Montelione, (C) 2010This Matlab Toolbox implements the FindCore algorithm described in Snyder, D.A.; Montelione, G.T. PROTEINS: Struct. Funct. Bioinformaticsm, 2005, 59: 673-86. Clustering algorithms for identifying core atom sets and for...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (41): Find Core Toolbox, version Download |
MOTIFINFO = GIBBSMOTIFSAMPLER(SEQARRAY,MOTIFVECTOR,ALPHABET,OPTIONS) Searches for the motifs in a set of sequences via Gibbs sampling. seqArray is a cell vector of sequence strings. motifVector is a vector of uniformly-spaced motif widths you wish to optimize. The program iterates over these...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (42): Gibbs Motif Sampler Download |
PDBRead is a function that will read a Protein Data Bank file into a MATLAB structure.PDB_struct = PDBRead(filename) reads the file corresponding to filename and stores the information contained in this file in the PDB_struct. e.g. PDB_struct = PDBRead('PDBSilk.txt')The file that is being read by...
Platforms: Matlab
License: Freeware | Size: 30.72 KB | Download (39): PDBRead Download |