Delaunay-based nonlocal interactions are sufficient and accurate in protein fold recognition

Authors

  • Mehdi Mirzaie,

    Corresponding author
    1. Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
    2. Department of Bioinformatics, School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
    • Correspondence to: Mehdi Mirzaie, Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19395-4618, Tehran, Iran. E-mail: mirzaie@ipm.ir

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  • Mehdi Sadeghi

    1. Department of Bioinformatics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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ABSTRACT

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.

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