SPServer: Split-statistical potentials for the analysis of protein structures and protein–protein interactions

Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes, Baldo Oliva*

*Awdur cyfatebol y gwaith hwn

Allbwn ymchwil: Cyfraniad at gyfnodolynErthygladolygiad gan gymheiriaid

7 Dyfyniadau (Scopus)
98 Wedi eu Llwytho i Lawr (Pure)

Crynodeb

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/.
Iaith wreiddiolSaesneg
Rhif yr erthygl4
Nifer y tudalennau13
CyfnodolynBMC Bioinformatics
Cyfrol22
Rhif cyhoeddi1
Dynodwyr Gwrthrych Digidol (DOIs)
StatwsCyhoeddwyd - 06 Ion 2021

Ôl bys

Gweld gwybodaeth am bynciau ymchwil 'SPServer: Split-statistical potentials for the analysis of protein structures and protein–protein interactions'. Gyda’i gilydd, maen nhw’n ffurfio ôl bys unigryw.

Dyfynnu hyn