ArticleBMC bioinformatics2021
SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- A roadmap for systematic humanization of a chimeric antigen receptor: preclinical validation of a humanized CD22 scFv as a model.Experimental hematology · 2026Article
- A review on computational models for predicting protein solubility.Journal of microbiology (Seoul, Korea) · 2025Review
- Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity inNAR genomics and bioinformatics · 2024Article
- ERMA (TMEM94) is a P-type ATPase transporter for MgMolecular cell · 2024Article
- Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology.BMC bioinformatics · 2024Article
- Computational prognostic evaluation of Alzheimer's drugs from FDA-approved database through structural conformational dynamics and drug repositioning approaches.Scientific reports · 2023Article
- SBILib: a handle for protein modeling and engineering.Bioinformatics (Oxford, England) · 2023Article
- In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface.International journal of molecular sciences · 2021Article
- Molecular docking analysis of p53 with Toll-like receptors.Bioinformation · 2021Article
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10 authors.
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Abstract
backgroundStatistical 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.
resultsHere, 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.
conclusionsWhile 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/ .
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