A beta-complex statistical four body contact potential combined with a hydrogen bond statistical potential recognizes the correct native structure from protein decoy sets
- Authors
- Sanchez-Gonzalez, Gilberto; Kim, Jae-Kwan; Kim, Deok-Soo; Garduno-Juarez, Ramon
- Issue Date
- Aug-2013
- Publisher
- WILEY
- Keywords
- beta-complex theory; energy potentials; four-body statistical potential; hydrogen bond statistical potential; improvement of decoy discrimination; protein structure prediction
- Citation
- PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, v.81, no.8, pp.1420 - 1433
- Indexed
- SCIE
SCOPUS
- Journal Title
- PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Volume
- 81
- Number
- 8
- Start Page
- 1420
- End Page
- 1433
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/162265
- DOI
- 10.1002/prot.24293
- ISSN
- 0887-3585
- 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 (-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. Proteins 2013; 81:1420-1433.
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