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UTOPIA (User-friendly Tools for Operating Informatics Applications) is a suite of free tools for visualising and analysing bioinformatics data. Based on an ontology-driven data model, it contains applications for viewing and aligning protein sequences, rendering complex molecular structures in 3D, and for finding and using resources such as web services and data objects.
Computational system for predicting protein subchloroplast locations from its primary sequence. It can locate the protein whose subcellular location is chloroplast in one of the four parts: envelope (which consists of outer membrane and inner membrane), thylakoid lumen, stroma and thylakoid membrane. (bio.tools entry) [97]
Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases. [ 1 ] [ 2 ] Mascot is widely used by research facilities around the world. Mascot uses a probabilistic scoring algorithm for protein identification that was adapted from the MOWSE algorithm.
The Molecular Operating Environment was developed by the Chemical Computing Group under the supervision of President/CEO Paul Labute. [3] Founded in 1994 [4] and based in Montreal, Quebec, Canada, this private company is dedicated to developing computation software that will challenge, revolutionize, and aid in the scientific methodology.
PEAKS Q is an add-on tool for protein quantification, supporting label (ICAT, iTRAQ, SILAC, TMT, 018, etc.) and label free techniques. SPIDER is a sequence tag based search tool within PEAKS, which deals with the possible overlaps between the de novo sequencing errors and the homology mutations.
The vast majority of modern systems biology modeling software support SBML, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support CellML , a standard used for representing physiological processes.
RaptorX is the successor to the RAPTOR protein structure prediction system. RAPTOR was designed and developed by Dr. Jinbo Xu and Dr. Ming Li at the University of Waterloo. RaptorX was designed and developed by a research group led by Prof. Jinbo Xu at the Toyota Technological Institute branch at Chicago.
APBS (previously also Advanced Poisson-Boltzmann Solver) is a free and open-source software for solving the equations of continuum electrostatics intended primarily for the large biomolecular systems. [1] [2] It is available under the BSD license. PDB2PQR prepares the protein structure files from Protein Data Bank for use with APBS.