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Optimal Ligand Descriptor for Pocket Recognition Based on the Beta-Shape

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  • Jae-Kwan Kim
  • Chung-In Won
  • Jehyun Cha
  • Kichun Lee
  • Deok-Soo Kim

Abstract

Structure-based virtual screening is one of the most important and common computational methods for the identification of predicted hit at the beginning of drug discovery. Pocket recognition and definition is frequently a prerequisite of structure-based virtual screening, reducing the search space of the predicted protein-ligand complex. In this paper, we present an optimal ligand shape descriptor for a pocket recognition algorithm based on the beta-shape, which is a derivative structure of the Voronoi diagram of atoms. We investigate six candidates for a shape descriptor for a ligand using statistical analysis: the minimum enclosing sphere, three measures from the principal component analysis of atoms, the van der Waals volume, and the beta-shape volume. Among them, the van der Waals volume of a ligand is the optimal shape descriptor for pocket recognition and best tunes the pocket recognition algorithm based on the beta-shape for efficient virtual screening. The performance of the proposed algorithm is verified by a benchmark test.

Suggested Citation

  • Jae-Kwan Kim & Chung-In Won & Jehyun Cha & Kichun Lee & Deok-Soo Kim, 2015. "Optimal Ligand Descriptor for Pocket Recognition Based on the Beta-Shape," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-29, April.
    • Handle: RePEc:plo:pone00:0122787
    DOI: 10.1371/journal.pone.0122787
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