Cavity Detecting the Protein-Ligand Binding Site

Introduction: CAVITY approach is used to detect the binding cavities of proteins and quantitatively calculate the ligandability and drugablity of a cavity. The CAVITY approach also acts as an independent module of our de novo drug design tool Ligbuilder 2.0.

Protein File (PDB):  
Parameter :     Separating Depth: Angstrom
 Reserving Depth: Angstrom
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Separating Depth: The defination of minimal depth of a binding site. Smaller value make more binding site link to each other by shallow area, vice versa.

Reserving Depth:The defination of maximal depth of a single binding site. Smaller value allow a lager binding site as a single binding site, vice versa.

Reference: Binding Site Detection and Druggability Prediction of Protein Targets for Structure-Based Drug Design, Current Pharmaceutical Design, Volume 19, Number 12, April 2013 , pp. 2326-2333.