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
- 김덕수
- Keywords
- beta-complex theory; energy potentials; four-body statistical potential; hydrogen bond statistical potential; improvement of decoy discrimination; protein structure prediction
- Issue Date
- 2013-08
- Publisher
- John Wiley & Sons, Ltd
- Citation
- PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 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
- https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.24293http://hdl.handle.net/20.500.11754/50036
- ISSN
- 0887-3585
- DOI
- 10.1002/prot.24293
- Appears in Collections:
- COLLEGE OF ENGINEERING[S](공과대학) > MECHANICAL ENGINEERING(기계공학부) > Articles
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