SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions.

Autor: Aguirre-Plans J; Structural Bioinformatics Lab, Department of Experimental and Health Science, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain., Meseguer A; Structural Bioinformatics Lab, Department of Experimental and Health Science, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain., Molina-Fernandez R; Structural Bioinformatics Lab, Department of Experimental and Health Science, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain., Marín-López MA; Structural Bioinformatics Lab, Department of Experimental and Health Science, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain., Jumde G; Structural Bioinformatics Lab, Department of Experimental and Health Science, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain., Casanova K; Structural Bioinformatics Lab, Department of Experimental and Health Science, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain., Bonet J; Laboratory of Protein Design and Immuno-Enginneering, School of Engineering, Ecole Polytechnique Federale de Lausanne, 1015, Lausanne, Vaud, Switzerland., Fornes O; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada., Fernandez-Fuentes N; Department of Biosciences, U Science Tech, Universitat de Vic-Universitat Central de Catalunya, Vic 08500, Barcelona, Catalonia, Spain.; Institute of Biological, Environ-Mental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK., Oliva B; Structural Bioinformatics Lab, Department of Experimental and Health Science, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain. baldo.oliva@upf.edu.
Jazyk: angličtina
Zdroj: BMC bioinformatics [BMC Bioinformatics] 2021 Jan 06; Vol. 22 (1), pp. 4. Date of Electronic Publication: 2021 Jan 06.
DOI: 10.1186/s12859-020-03770-5
Abstrakt: Background: Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we decomposed the statistical potentials in different terms, named Split-Statistical Potentials, accounting for the type of amino acid pairs, their hydrophobicity, solvent accessibility and type of secondary structure. These potentials have been successfully used to identify near-native structures in protein structure prediction, rank protein docking poses, and predict PPI binding affinities.
Results: Here, we present the SPServer, a web server that applies the Split-Statistical Potentials to analyze protein folds and protein interfaces. SPServer provides global scores as well as residue/residue-pair profiles presented as score plots and maps. This level of detail allows users to: (1) identify potentially problematic regions on protein structures; (2) identify disrupting amino acid pairs in protein interfaces; and (3) compare and analyze the quality of tertiary and quaternary structural models.
Conclusions: While there are many web servers that provide scoring functions to assess the quality of either protein folds or PPI structures, SPServer integrates both aspects in a unique easy-to-use web server. Moreover, the server permits to locally assess the quality of the structures and interfaces at a residue level and provides tools to compare the local assessment between structures. SERVER ADDRESS: https://sbi.upf.edu/spserver/ .
Databáze: MEDLINE
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