New statistical potential for quality assessment of protein models and a survey of energy functions

Dmitry Rykunov, Andras Fiser

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Background: Scoring functions, such as molecular mechanic forcefields and statistical potentials are fundamentally important tools in protein structure modeling and quality assessment.Results: The performances of a number of publicly available scoring functions are compared with a statistical rigor, with an emphasis on knowledge-based potentials. We explored the effect on accuracy of alternative choices for representing interaction center types and other features of scoring functions, such as using information on solvent accessibility, on torsion angles, accounting for secondary structure preferences and side chain orientation. Partially based on the observations made, we present a novel residue based statistical potential, which employs a shuffled reference state definition and takes into account the mutual orientation of residue side chains. Atom- and residue-level statistical potentials and Linux executables to calculate the energy of a given protein proposed in this work can be downloaded from http://www.fiserlab.org/potentials.Conclusions: Among the most influential terms we observed a critical role of a proper reference state definition and the benefits of including information about the microenvironment of interaction centers. Molecular mechanical potentials were also tested and found to be over-sensitive to small local imperfections in a structure, requiring unfeasible long energy relaxation before energy scores started to correlate with model quality.

Original languageEnglish (US)
Article number128
JournalBMC Bioinformatics
Volume11
DOIs
StatePublished - Mar 12 2010

Fingerprint

Quality Assessment
Energy Function
Scoring
Proteins
Protein
Molecular mechanics
Energy
Molecular Mechanics
Torsional stress
Force Field
Imperfections
Linux
Protein Structure
Secondary Structure
Knowledge-based
Accessibility
Interaction
Model
Correlate
Torsion

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Cite this

New statistical potential for quality assessment of protein models and a survey of energy functions. / Rykunov, Dmitry; Fiser, Andras.

In: BMC Bioinformatics, Vol. 11, 128, 12.03.2010.

Research output: Contribution to journalArticle

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