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Protein & Peptide Letters


ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

Identification of Ligand-Binding Pockets in Proteins Using Residue Preference Methods

Author(s): Zhijun Qiu and Xicheng Wang

Volume 16, Issue 8, 2009

Page: [984 - 990] Pages: 7

DOI: 10.2174/092986609788923284

Price: $65


Identification of ligand-binding pockets in proteins is pivotal to protein function definition and drug discovery. In this study, we focus on determining the binding pockets in proteins for potential ligands without any a priori knowledge. Three methods based upon residue preference concept are proposed to predict ligand-binding pockets, where we deal with three types of residue preference (residue based, atom based and atom-contact-pair based preference), respectively. Two test sets were chosen to examine the proposed methods. Two different identification rules (named Top1 and Top2) are used to detect ligand-binding pockets. The results show that the atom-contact-pair method has good accuracy and high efficiency, better than the other two methods. By means of preference analysis for amino acids and atom-contactpairs, we find that Gly and atom-contact-pairs on aromatic residues appear at ligand-binding pockets more frequently. The former favors pocket flexibility, and the latter shows that aggregate hydrophobic surface may play an important role in complex formation.

Keywords: Residue preference, ligand-binding pocket identification, atom-contact-pair

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