Excess Protein

An open source implementation of a protein threading program based on the energy functions and techniques originally introduced by Prospect.

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

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

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

'Proteins' is a database for protein sequences. A tool that many scientists need every day. Very often, sequences of proteins have to be looked up quickly or properties like extinction coefficients have to be calculated. 'Proteins' neatly arranges your fa


Platforms: Mac

The Ablebits Trim Spaces for Excel add-in will quickly remove leading and trailing spaces from your cells. Follow three simple steps to have your Excel worksheets ready for further work. - In your Excel worksheet, select the cells, columns or rows from which you want to remove excess...


Platforms: Windows

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

Earth albedo is the sunlight reflected off the Earth's surface. The Earth albedo induces power in solar cells on spacecrafts just like direct sunlight. The Earth Albedo Toolbox may be used to calculate the amount of Earth albedo arriving at an object in space, maintaining information of direction...


Platforms: Matlab

The self-contained script demonstrates excess, volatility driven growth, in a rebalanced portfolio.Based on the paper "Benchmarking and Rebalancing" by Gabay and Herlemont, yats.com, 19 Septembre 2007, this script reproduces example 1, showing the long-term rebalancing excess growth rate g*.There...


Platforms: Matlab

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

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

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

Based on Physica A 375 (2007) 365d-deOCt373.'g' must be the adjacency matrix of the graph of interest.It has not been verified because the Helicobacter pylori protein interaction graph used as the example in the article could not be obtained.


Platforms: Matlab