An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure

Bhagavat, Raghu and Sankar, Santhosh and Srinivasan, Narayanaswamy and Chandra, Nagasuma (2018) An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure. In: STRUCTURE, 26 (3). 499+.

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Abstract

Protein-ligand interactions form the basis of most cellular events. Identifying ligand binding pockets in proteins will greatly facilitate rationalizing and predicting protein function. Ligand binding sites are unknown for many proteins of known three-dimensional (3D) structure, creating a gap in our understanding of protein structure-function relationships. To bridge this gap, we detect pockets in proteins of known 3D structures, using computational techniques. This augmented pocketome (PocketDB) consists of 249,096 pockets, which is about seven times larger than what is currently known. We deduce possible ligand associations for about 46% of the newly identified pockets. The augmented pocketome, when subjected to clustering based on similarities among pockets, yielded 2,161 site types, which are associated with 1,037 ligand types, together providing fold-site-type-ligand-type associations. The PocketDB resource facilitates a structure-based function annotation, delineation of the structural basis of ligand recognition, and provides functional clues for domains of unknown functions, allosteric proteins, and druggable pockets.

Item Type:	Journal Article
Publication:	STRUCTURE
Publisher:	CELL PRESS, 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA
Additional Information:	Copy right for the article belong to CELL PRESS, 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA
Department/Centre:	Division of Biological Sciences > Biochemistry Division of Biological Sciences > Molecular Biophysics Unit Division of Physical & Mathematical Sciences > Mathematics
Date Deposited:	02 Apr 2018 19:57
Last Modified:	11 Oct 2018 14:05
URI:	http://eprints.iisc.ac.in/id/eprint/59448

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