Protein Similarity

FastSemSim is specially designed as a handy Python-based efficient implementation of a couple of semantic similarity measures. The main target of the project is to enable fast and easy calculation of similarity between proteins and genes using the Gene Ontology

Similarity is a useful program that helps you to find and remove similar, duplicate musical files (MP3, WMA, OGG, ASF, WAV, FLAC, APE, WV) with the same or similar sound content, music tags (ID3,WMF,Vorbis). This is the best program where similarity of a sound part is checked, not just music tags...

WordNet::Similarity::Visual is a Perl extension for providing visualization tools for WordNet::Similarity. SYNOPSIS Basic Usage Example use WordNet::Similarity::Visual; $gui = WordNet::Similarity::Visual->new; $gui->initialize; This package provides a graphical extension for...


Platforms: *nix

WordNet::Similarity::PathFinder is a Perl module to implement path finding methods (by node counting) for WordNet::Similarity measures of semantic relatedness. SYNOPSIS use WordNet::QueryData; my $wn = WordNet::QueryData->new; use WordNet::Similarity::PathFinder; my $obj =...


Platforms: *nix

WordNet::Similarity::vector_pairs is a Perl module for computing semantic relatedness of word senses using second order co-occurrence vectors of glosses of the word senses. SYNOPSIS use WordNet::Similarity::vector_pairs; use WordNet::QueryData; my $wn = WordNet::QueryData->new(); my...


Platforms: *nix

WordNet::Similarity is a collection of Perl modules for computing measures of semantic relatedness. SYNOPSIS Basic Usage Example use WordNet::QueryData; use WordNet::Similarity::path; my $wn = WordNet::QueryData->new; my $measure = WordNet::Similarity::path->new ($wn); my $value =...


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

This module allows the administrator to create a wide ranging set of similarity calculations. It can out of the box, calculate similar nodes of a specific type using the search index, taxonomy terms and node title. These similarities are calculated on cron run.This module is in the middle of a...


Platforms: PHP

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

Similarity Evaluator is a tool to analyse similarity function implementations and algorithms, where is possible to compare several APIs on performance, best result, similarity and discernability values.


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

Function calculates cosine cross-similarity between time series of threshold crossings with time lags. It also calculates dominant lag and maximum value.More detailshttp://www.ida.liu.se/~agbur/Software.htm


Platforms: Matlab

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

Function calculates window cross-similarity between time series of threshold crossings for selected window span. Correlation between high temporal resolution records aggregated over time for records of original resolution.More informationhttp://www.ida.liu.se/~agbur/Software.htm


Platforms: Matlab