Pocket2 Receptor-based Pharmacophore Model

Introduction: Pocket v.2 has been developed based on the original Pocket module in the de novo drug design program LigBuilder. Pocket v.2 is able to derive a pharmacophore model directly from a given protein-ligand complex structure without human intervention. Key features in the pharmacophore model are automatically reduced to a reasonable number.


Cavity File (PDB):  
Vacant File (PDB):  
With Ligand:  
Ligand File (MOL2):  
User Information:     Your name:
 Your email:

Cavity File and Vacant File: They are outputs of Cavity, you may find it here. Cavity may output multiple cavitys and you should choose the right one manually.

With Ligand: You may generate the pharmacophore model either with the aid of a ligand or not. The ligand should have proper orientation and conformation, so that pharmacophore features ultilized by the ligand would be stressed.


This is the online version of Pocket V.2 programs, you can also download the Pocket V.2 program in our download site.

Reference to Pocket V.2:
J Chen, LH Lai, Pocket v.2: Further Developments on Receptor-Based Pharmacophore Modeling, J. Chem. Inf. Model., 2006,46(6),2684-2691.