Paper Info
Title
Protein-ligand binding site detection as an alternative route to molecular docking and drug repurposing.
Abstract
After the onset of the genomic era, the detection of ligand binding sites in proteins has emerged over the last few years as a powerful tool for protein function prediction. Several approaches, both sequence and structure based, have been developed, but the full potential of the corresponding tools has not been exploited yet. Here, we describe the development and classification of a large, almost exhaustive, collection of protein-ligand binding sites to be used, in conjunction with the Ligand Binding Site Recognition Application Web Application developed in our laboratory, as an alternative to virtual screening through molecular docking simulations to identify novel lead compounds for known targets. Ligand binding sites derived from the Protein Data Bank have been clustered according to ligand similarity, and given a known ligand, the binding mode of related ligands to the same target can be predicted. The collection of ligand binding sites contains more than 200,000 sites corresponding to more than 20,000 different ligands. Furthermore, the ligand binding sites of all Food and Drug Administration-approved drugs have been classified as well, allowing to investigate the possible binding of each of them (and related compounds) to a given target for drug repurposing and redesign initiatives. Sample usage cases are also described to demonstrate the effectiveness of this approach.
Year
DOI
Venue
2018
10.1515/bams-2018-0004
BIO-ALGORITHMS AND MED-SYSTEMS
Keywords
Field
DocType
drug repurposing,FDA-approved drugs,ligand binding site recognition,ligand binding sites
Protein ligand,Docking (molecular),Drug repositioning,Binding site,Chemistry,Computational biology
Journal
Volume
Issue
ISSN
14
2
1895-9091
Citations 
PageRank 
References 
0
0.34
13
Authors
3
Name
Order
Citations
PageRank
Daniele Toti110513.86
Gabriele Macari200.68
Fabio Polticelli3688.97