Identi fication of Pockets on Protein Surface to Predict Protein–Ligand Binding Sites - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 24

Chapter 2
Identification of Pockets on Protein Surface
to Predict Protein-Ligand Binding Sites

Bingding Huang

Keywords LIGSITE csc ￿ MetaPocket ￿ Pocket identi fi cation ￿ Protein-ligand bind-
ing sites ￿ 3D grid ￿ Residues conservation ￿ Cavity ￿ Pocket ￿ Mathematical mor-
phology ￿ Q-SiteFinder ￿ Inside protein ￿ Near surface ￿ In solvent ￿ Cubic
diagonals

2.1 Introduction

Proteins perform their biological functions in different cell processes mainly by
interacting with other molecules such as other proteins, ligands, DNAs and RNAs
etc. Not all but only parts of residues in proteins are involved in such interactions.
Therefore, identification of these interacting residues on a protein is of great impor-
tance to understanding of protein functions. In the variety of interactions, the inter-
actions between proteins and ligands have been widely studied in protein-ligand
docking, in virtual screening and structure-based drug design etc. There exist a
number of cavities or pocket sites on protein surface where small molecules might
bind. Therefore, identification of such pocket sites is often the first step in protein
ligand-binding site prediction. Many computational algorithms and tools have been
developed in recent decades to predict protein-ligand binding site from identi fi -
cation of pockets on protein structures, such as POCKET (Levitt and Banaszak
1992 ), LIGSITE (Hendlich et al. 1997 ), CAST (Dundas et al. 2006 ; Binkowski et al.
2003 ) , LIGSITE CS/C (Huang and Schroeder 2006 ), PASS (Brady and Stouten 2000 ) ,

B. Huang ( * )
Systems Biology Division, Zhejiang-California International NanoSystems Institute,
Zhejiang University , Kaixuan Road 268 , 310029 Hangzhou , China
Bioinformatics Group, Biotechnology Center, Technical University of Dresden,
Tatzberg 47 , 01307 Dresden , Germany
e-mail: [e-mail]