A beta-complex statistical four body contact potential combined with a hydrogen bond statistical potential recognizes the correct native structure from protein decoy sets

Gilberto Sánchez-González, Jae Kwan Kim, Deok Soo Kim, Ramón Garduño-Juárez

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

We present a new four-body knowledge-based potential for recognizing the native state of proteins from their misfolded states. This potential was extracted from a large set of protein structures determined by X-ray crystallography using BetaMol, a software based on the recent theory of the beta-complex (β-complex) and quasi-triangulation of the Voronoi diagram of spheres. This geometric construct reflects the size difference among atoms in their full Euclidean metric; property not accounted for in a typical 3D Delaunay triangulation. The ability of this potential to identify the native conformation over a large set of decoys was evaluated. Experiments show that this potential outperforms a potential constructed with a classical Delaunay triangulation in decoy discrimination tests. The addition of a statistical hydrogen bond potential to our four-body potential allows a significant improvement in the decoy discrimination, in such a way that we are able to predict successfully the native structure in 90% of cases.

Original languageEnglish
Pages (from-to)1420-1433
Number of pages14
JournalProteins: Structure, Function and Bioinformatics
Volume81
Issue number8
DOIs
StatePublished - 2013 Aug 1

Keywords

  • Beta-complex theory
  • Energy potentials
  • Four-body statistical potential
  • Hydrogen bond statistical potential
  • Improvement of decoy discrimination
  • Protein structure prediction

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