Impact of protein binding cavity volume (PCV) and ligand volume (LV) in rigid and flexible docking of protein–ligand complexes

• Published in: Bioorganic & medicinal chemistry letters 2012-12, Vol.22 (24), p.7593-7597
• Main Authors: Saranya, N., Jeyakanthan, J., Selvaraj, S.
• Format: Article
• Language: English
• Subjects: Binding Sites - drug effects; Biological and medical sciences; crystal structure; Docking and scoring; Ligands; Medical sciences; Models, Molecular; Pharmacology. Drug treatments; protein binding; Protein binding cavity volume; protein conformation; Protein flexibility; proteins; Proteins - chemistry; Structure-Activity Relationship; Structure-based drug design
• ISSN: 0960-894X; 1464-3405
• DOI: 10.1016/j.bmcl.2012.10.018

The importance of protein binding cavity volume (PCV) and ligand volume (LV) in rigid and flexible docking has been studied in 48 protein–ligand complexes belonging to eight protein families. In continuation of our earlier study on protein flexibility in relationship to PCV and LV, this study analyzes the importance of PCV and LV in the scoring and ranking of ligands in docking experiments. Crystal structures of protein–ligand complexes with varied PCV were chosen for docking ligands of varied volume in each protein family. Docking and scoring accuracy have been evaluated by self and cross docking of ligands to the given protein conformation. Effect of PCV and LV in rigid and flexible docking has been studied both in apo and holo proteins. Rigid docking has performed well when appropriate protein conformation is used. Selecting the proteins with appropriate PCV based on the LV information is suggested for better results in ensemble docking.