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Delaunay‐based nonlocal interactions are sufficient and accurate in protein fold recognition
Author(s) -
Mirzaie Mehdi,
Sadeghi Mehdi
Publication year - 2014
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24407
Subject(s) - delaunay triangulation , tessellation (computer graphics) , mathematics , computer science , physics , statistical physics , combinatorics , crystallography , geometry , chemistry
This study is aimed at showing that considering only nonlocal interactions (interactions of two atoms with a sequence separation larger than five amino acids) extracted using Delaunay tessellation is sufficient and accurate for protein fold recognition. An atomic knowledge‐based potential was extracted based on a Delaunay tessellation with 167 atom types from a sample of the native structures and the normalized energy was calculated for only nonlocal interactions in each structure. The performance of this method was tested on several decoy sets and compared to a method considering all interactions extracted by Delaunay tessellation and three other popular scoring functions. Features such as the contents of different types of interactions and atoms with the highest number of interactions were also studied. The results suggest that considering only nonlocal interactions in a Delaunay tessellation of protein structure is a discrete structure catching deep properties of the three‐dimensional protein data. Proteins 2014; 82:415–423. © 2013 Wiley Periodicals, Inc.