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NTIS 바로가기Proteins, v.81 no.8, 2013년, pp.1420 - 1433
Sánchez‐González, Gilberto (Facultad de Ciencias, Universidad Autó) , Kim, Jae‐Kwan (noma del Estado de Morelos, Av. Universidad 1001, Cuernavaca, Morelos, 62209, Mé) , Kim, Deok‐Soo (xico) , Garduño‐Juárez, Ramón (Voronoi Diagram Research Center, Department of Industrial Engineering, Hanyang University, Seoul, Korea)
ABSTRACTWe 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. Proteins 2013; 81:1420–1433. © 2013 Wiley Periodicals, Inc.
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