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Swiss-model (stylized as SWISS-MODEL) is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. [ 1 ] [ 2 ] As of 2024 [update] , homology modeling is the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications.
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). [2] [3] It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability ...
In 2000, maintenance of the software moved to the Dutch Center for Molecular and Biomolecular Informatics (CMBI) in Nijmegen, Netherlands. [1] It is available for in-house use, or as a web-based resource. [4] As of February 2022, the original paper describing WHAT IF has been cited more than 4,000 times.
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.
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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.
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects.It contains a large amount of information about the biological function of proteins derived from the research literature.