Search Results for "protein"

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab...

APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

CUDASW++ software is a public open source software for Smith-Waterman protein database searches on Graphics Processing Units with CUDA. This software have been added to the NVIDIA Tesla Bio Workbench (http://www.nvidia.com/object/swplusplus_on_tesla.html

A suite of statistically-based programs for inferring joint sequence-structural determinants of protein functional specificity written in C/C++ within a linux environment.

Chou & Fasman algorithm implemented using C language. It is a CUI tool used for protein secondary structure prediction.

AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected...

PSICOV (Protein Sparse Inverse Covariance estimation program) is a coevoultion algorithm applied to very large (typically >=1000 sequences) multiple sequence alignments for precise protein structural contact prediction. This is the unofficial precompiled Windows binary for PSICOV compiled by Chengxin Zhang at Fudan University. The source code is copyrighted by David T. Jones, University College London.

This space is not maintained anymore. If you want to get the latest updates on fpocket refer to https://github.com/Discngine/fpocket. Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

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

MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/

MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/

FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.

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.

PocketDepth helps determine binding grooves for protein molecules. Applicable in Bioinformatics and Drug discovery. Literature - http://www.ncbi.nlm.nih.gov/pubmed/17949996 Author's thesis - http://openwetware.org/wiki/Kalidas_Y

The C Protein Folding Library is a minimalistic, high-performance modular library of C functions and data structures for computing folding simulations of proteins on a wide variety of computer hardware.

EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)

The project implements Protein Folding on a CBE. The role of water on folding under different environments is studied through visualization results. It acts as a tool to visualize the folding of an amino acid sequence into a 3D protein structure.

Protein-Protein Interaction Literature Visualization System

RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats. Radar has moved to github (https://github.com/AndreasHeger/radar)

Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.

ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.

Basic implementation of K-nearest neighbour Algorithm and the application of KNN to classify protein sequences as transmembrane beta barrel or non-transmembrane beta barrel on the basis of whole sequence amino acid composition given as input.

ProteinFinder - a C language parallel computing engine for tandem protein mass spectrometry database search. ProteinFinder is interfaced with MySQL relational database MassSpec that hosts the experimental data, predicted databases, and search results.