Protein–protein structure prediction by scoring molecular dynamics trajectories of putative poses

Edoardo Sarti, Ivan Gladich, Stefano Zamuner, Bruno E. Correia, Alessandro Laio

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

The prediction of protein–protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based on searching the structure corresponding to the global minimum of a suitable scoring function. However, protein complexes are often highly flexible, with mobile side chains and transient contacts due to thermal fluctuations. Flexibility can be neglected if one aims at finding quickly the approximate structure of the native complex, but may play a role in structure refinement, and in discriminating solutions characterized by similar scores. We here benchmark the capability of some state-of-the-art scoring functions (BACH-SixthSense, PIE/PISA and Rosetta) in discriminating finite-temperature ensembles of structures corresponding to the native state and to non-native configurations. We produce the ensembles by running thousands of molecular dynamics simulations in explicit solvent starting from poses generated by rigid docking and optimized in vacuum. We find that while Rosetta outperformed the other two scoring functions in scoring the structures in vacuum, BACH-SixthSense and PIE/PISA perform better in distinguishing near-native ensembles of structures generated by molecular dynamics in explicit solvent. Proteins 2016; 84:1312–1320.

Original languageEnglish
Pages (from-to)1312-1320
Number of pages9
JournalProteins: Structure, Function and Bioinformatics
Volume84
Issue number9
DOIs
Publication statusPublished - 1 Sep 2016
Externally publishedYes

Fingerprint

Molecular Dynamics Simulation
Vacuum
Molecular dynamics
Trajectories
Benchmarking
Protein Conformation
Proteins
Hot Temperature
Temperature
Conformations
Monomers
Computer simulation

Keywords

  • BACH-SixthSense
  • comparative study
  • MD
  • native discrimination
  • PIE/PISA
  • protein–protein interaction
  • refinement
  • rigid docking
  • Rosetta
  • scoring function

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Cite this

Protein–protein structure prediction by scoring molecular dynamics trajectories of putative poses. / Sarti, Edoardo; Gladich, Ivan; Zamuner, Stefano; Correia, Bruno E.; Laio, Alessandro.

In: Proteins: Structure, Function and Bioinformatics, Vol. 84, No. 9, 01.09.2016, p. 1312-1320.

Research output: Contribution to journalArticle

Sarti, Edoardo ; Gladich, Ivan ; Zamuner, Stefano ; Correia, Bruno E. ; Laio, Alessandro. / Protein–protein structure prediction by scoring molecular dynamics trajectories of putative poses. In: Proteins: Structure, Function and Bioinformatics. 2016 ; Vol. 84, No. 9. pp. 1312-1320.
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