ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
Fabian Glaser,Tal Pupko,Inbal Paz,Rachel E. Bell,Dalit Bechor-Shental,Eric Martz,Nir Ben-Tal +6 more
TLDR
A new web server, ConSurf, is presented, which automates algorithms for the identification of functionally important regions in proteins of known three dimensional structure by estimating the degree of conservation of the amino-acid sites among their close sequence homologues.Abstract:
UNLABELLED We recently developed algorithmic tools for the identification of functionally important regions in proteins of known three dimensional structure by estimating the degree of conservation of the amino-acid sites among their close sequence homologues. Projecting the conservation grades onto the molecular surface of these proteins reveals patches of highly conserved (or occasionally highly variable) residues that are often of important biological function. We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins. AVAILABILITY The ConSurf web server is available at:http://consurf.tau.ac.il. SUPPLEMENTARY INFORMATION A set of examples is available at http://consurf.tau.ac.il under 'GALLERY'.read more
Citations
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ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
TL;DR: Several new features into ConSurf are introduced, including automatic selection of the best evolutionary model used to infer the rates, the able to homology-model query proteins, prediction of the secondary structure of query RNA molecules from sequence, the ability to view the biological assembly of a query (in addition to the single chain), mapping of the conservation grades onto 2D RNA models and an advanced view of the phylogenetic tree.
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ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
TL;DR: The new version of the ConSurf web server is presented, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process, and calculates the evolutionary rates for nucleic acid sequences.
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ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
TL;DR: This new version of ConSurf includes an empirical Bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release and includes a measure of confidence for the inferred amino acid conservation scores.
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Superoxide dismutases and superoxide reductases
Yuewei Sheng,Isabel A. Abreu,Diane E. Cabelli,Michael J. Maroney,Anne-Frances Miller,Miguel Teixeira,Joan Selverstone Valentine,Joan Selverstone Valentine +7 more
TL;DR: The SORs and three very different types of SOD enzymes are redox-active metalloenzymes that have evolved entirely independently from one another for the purpose of lowering superoxide concentrations, suggesting that, from the start of the rise of O2 on Earth, the chemistry of superoxide has been an important factor during evolution.
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ProFunc: a server for predicting protein function from 3D structure
TL;DR: ProFunc () is a web server for predicting the likely function of proteins whose 3D structure is known but whose function is not, and makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins.
References
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Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
TL;DR: A novel method is presented, 'Rate4Site', which maps the rate of evolution among homologous proteins onto the molecular surface of one of the homologues whose 3D-structure is known, using the maximum likelihood (ML) principle.