Analyzing Protein

ProDy is a free and open-source Python package for analyzing protein structural dynamics. It allows for quantitative analysis of heterogeneous experimental structural datasets and comparison with theoretically predicted conformational dynamics. The input for ProDy is the atomic coordinates of... Platforms: *nix

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... Platforms: Matlab

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

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

ADMLogger is a log analyzing engine based on fireparse. After I had written fireparse, I had found myself writing little scripts based on it. Like one that told me what my FTP server did that day. And then more things like - were unauthorized machines trying to get IP addresses from my DHCP... Platforms: *nix

Unicode Utilities project are a set of programs for manipulating and analyzing Unicode text. uniname defaults to printing the character offset of each character, its byte offset, its hex code value, its encoding, the glyph itself, and its name. Command line options allow undesired information to... Platforms: *nix

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

TreeSize for Unix is a disk consumption analyzing tool, which sorts folders according to their physical occupied sizes. The perfect tool to help you obtaining more disk free space, on your hard drive, usb pen drive or even on network folders (provided that they are mounted and you have access... Platforms: *nix

Now you can find out without even logging into the box by only analyzing the packets on the network! Every wonder if someone is remotely logging in to one of your boxen and then going on to another? Now you can find out without even logging into the box by only analyzing the packets on the... Platforms: *nix

gpss is a gnuplot front end for analyzing snort perfmonitor log files. It offers both 2D and 3D interactive or batch graphing of things like bits per second, packets per second, drop percentage, fragments per second, and more. gpss project is useful as both a performance evaluation tool or a... 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