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

BMC Bioinformatics. 2021 Jan 6;22(1):4. doi: 10.1186/s12859-020-03770-5.


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/ .

Keywords: Knowledge-based potential; Protein structure evaluation; Protein structure prediction; Protein structure quality assessment; Protein–protein evaluation; Protein–protein interaction.

MeSH terms

  • Amino Acids / chemistry
  • Amino Acids / metabolism
  • Internet
  • Knowledge Bases
  • Models, Statistical
  • Protein Interaction Maps / physiology*
  • Protein Structure, Secondary*
  • Proteins* / chemistry
  • Proteins* / metabolism
  • Software*


  • Amino Acids
  • Proteins