Protein

This contest concerns a very simplified two-dimensional version of the protein folding problem. Given the amino acid sequence of a simplified protein, your job is to determine a final "optimally folded" configuration. Each potential arrangement of the protein sequence is associated with an energy...

An interactive simulation of protein folding that allows you to fold proteins of your own design.

HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures. Features . Protein Structure Quality...


Platforms: *nix

CLC Protein Workbench is a scientific application for bioinformation, aimed at the advanced analysis of protein sequences. This program offers you a really wide range of analyses, all of them integrated in the same interface, which is very friendly and accessible to all users.The options and...


Platforms: Windows

Protein BLAST Widget provides a quick access to the Protein Basic Local Alignment Search Tool at NCBI. You just have to type or paste your sequence and to select the program to be used.


Platforms: Mac

GRaPe - a platform-independent software tool for building integrative gene-reaction-protein (GRP) networks. It generates the kinetic equations for each reaction and outputs a SBML document. It also implements two methods for parameter estimation.


Platforms: Windows, Mac, Linux

User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files


Platforms: Windows, Mac, Linux

The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.


Platforms: Windows, Mac, Linux

Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files


Platforms: Windows, Mac, Linux

The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm.


Platforms: Windows, Mac, BSD, Linux

The sixth MATLAB Programming Contest, Protein, will run from November 6-13, 2002.This contest concerns a very simplified two-dimensional version of the protein folding problem. Given the amino acid sequence of a simplified protein, your job is to determine a final "optimally folded"...


Platforms: Matlab

This program is a bioinformatics tool developed for helping biologists finding patterns from a set of protein sequences. The method is the first one that fully utilizes the advantages of the Dirichlet mixture models. It starts from a random pattern and iteratively improves the Bayesian log-odds...


Platforms: Matlab

Allows the user to calculate her optimum post-workout protein shake recipe and determine right mixture of these three essential ingredients, plus her daily recommended protein dose: 1. Protein 2. Carbohydrate 3. WaterAll calculations are based on her body weight. Install : 1. Unzip the...


Platforms: PHP

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =...


Platforms: *nix

PROMPT is a system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatic data retrieval and integration, many analysis and comparison algorithms, and a full-featured GUI application. Exhaustive statistical...


Platforms: *nix

The Protein Molar Converter widget is a Dashboard widget that allows to perform molar conversions for proteins according to size.


Platforms: Mac

ProtAnnot is a small, Java based application is a protein annotation viewer that displays protein annotations in the context of the genomic sequence. This software is a making it easy to see how alternative mRNA structures affect the various protein products encoded at a locus. for WindowsAll


Platforms: Windows

The Genome Positioning System (GPS) is a software tool to study protein-DNA interaction using ChIP-Seq data. GPS builds a probabilistic mixture model to predict the most likely positions of binding events at single-base resolution. GPS is a Java software, so it runs on multiple platforms,...


Platforms: Windows

TMRPres2D or TransMembrane protein Re-Presentation in 2 Dimensions for long, is a small, easy to use application designed to automate the creation of uniform, two-dimensional, high analysis graphical images/models of alpha-helical or beta-barrel transmembrane proteins. Protein sequence data and...


Platforms: Windows

Main Workbench includes all features from CLC DNA Workbench, CLC RNA Workbench, and CLC Protein Workbench, as well as a range of Gene Expression Analysis. CLC Main Workbench creates a software environment enabling users to make a large number of advanced protein sequence analyses, combined with...


Platforms: Windows, XP, Windows Vista, XPX64, 7, 7x64