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

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
Author
김재관
Keywords
beta-complex theory; energy potentials; four-body statistical potential; hydrogen bond statistical potential; improvement of decoy discrimination; protein structure prediction; QUASI-CHEMICAL APPROXIMATION; GLOBULAR-PROTEINS; MEAN FORCE; DEPENDENT CONTRIBUTIONS; DELAUNAY TESSELLATION; STRUCTURE PREDICTION; RESIDUE POTENTIALS; PAIR POTENTIALS; PACKING DENSITY; ENERGY FUNCTION
Issue Date
2013-06
Publisher
John Wiley & Sons, Ltd
Citation
Proteins: Structure, Function and Bioinformatics, August 2013, 81(8), p.1420-1433
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. (c) 2013 Wiley Periodicals, Inc.
URI
http://onlinelibrary.wiley.com/doi/10.1002/prot.24293/abstracthttp://hdl.handle.net/20.500.11754/45620
ISSN
0887-3585
DOI
10.1002/prot.24293
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ETC[S] > 연구정보
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