A holistic in silico approach to predict functional sites in protein structures

Bioinformatics
Joan SeguraNarcis Fernandez-Fuentes

Abstract

Proteins execute and coordinate cellular functions by interacting with other biomolecules. Among these interactions, protein-protein (including peptide-mediated), protein-DNA and protein-RNA interactions cover a wide range of critical processes and cellular functions. The functional characterization of proteins requires the description and mapping of functional biomolecular interactions and the identification and characterization of functional sites is an important step towards this end. We have developed a novel computational method, Multi-VORFFIP (MV), a tool to predicts protein-, peptide-, DNA- and RNA-binding sites in proteins. MV utilizes a wide range of structural, evolutionary, experimental and energy-based information that is integrated into a common probabilistic framework by means of a Random Forest ensemble classifier. While remaining competitive when compared with current methods, MV is a centralized resource for the prediction of functional sites and is interfaced by a powerful web application tailored to facilitate the use of the method and analysis of predictions to non-expert end-users. http://www.bioinsilico.org/MVORFFIP

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Citations

Oct 8, 2013·The Protein Journal·Yee Siew ChoongTheam Soon Lim
Oct 16, 2012·Briefings in Bioinformatics·Santo Motta, Francesco Pappalardo
Nov 19, 2013·PloS One·Ramaswamy RakshambikaiKoodali Thazath Nishant
Aug 3, 2013·Biochimica Et Biophysica Acta·Bing NiuJinyuan Yin
May 15, 2015·Briefings in Bioinformatics·Reyhaneh EsmaielbeikiCharlotte M Deane
Jul 19, 2018·Bioinformatics·Ruben Sanchez-GarciaJoan Segura
Feb 27, 2020·Current Topics in Medicinal Chemistry·Olivia SlaterMaria Kontoyianni
Jun 11, 2016·Biochemical Society Transactions·Daniel PoglayenNarcis Fernandez-Fuentes
Jun 15, 2019·Proteins·Chloé DequekerAlessandra Carbone
Jun 18, 2019·Journal of Molecular Biology·Eric T C Wong, Jörg Gsponer
Sep 26, 2020·Journal of Molecular Biology·Patricia Mirela-BotaNarcis Fernandez-Fuentes
Jul 23, 2021·Journal of Chemical Information and Modeling·Igor Kozlovskii, Petr Popov

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