title: A beta-complex statistical four body contact potential combined with a hydrogen bond statistical potential recognizes the correct native structure from protein decoy sets.
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.
authors.affiliation: Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.
authors.forename: Gilberto
authors.initials: G
authors.lastname: Sánchez-González
authors.forename: Jae-Kwan
authors.initials: JK
authors.lastname: Kim
authors.forename: Deok-Soo
authors.initials: DS
authors.lastname: Kim
authors.forename: Ramón
authors.initials: R
authors.lastname: Garduño-Juárez
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
keywords: beta-complex theory; energy potentials; four-body statistical potential; hydrogen bond statistical potential; improvement of decoy discrimination; protein structure prediction