Modeling, Docking and Virtual Screening

The SMSSF is equipped to screen millions of small molecules in receptor candidates with in silico docking. This service is led by Dr. Ken Satyshur who has over 20 years experience in molecular modeling for drug discovery and computational methods for lead optimization. 

A target protein is first examined for probable sites for docking using a Stereo 3D Dell T5500 molecular graphics computer (Intel dual quad, Nvidia FX 4800 graphics) and the Sybyl molecular-modeling visualization software. The best receptor sites are then screened using the Sybyl-implemented Surflex molecular docking package from the S. Jain lab on a Dell 3950 server (Intel dual quad core) running Sybyl with 14 engines for computation.  The small molecule compounds are taken from established databases such as Chembridge, Maybridge and Life Sciences in the ZINC public database.  Databases enriched through Surflex docking are examined with 3D graphics to select the best 1-2% for further docking with Autodock4 from Scripps Institute.  Docking with Autodock4 can be done on the 40 cores at the SMSSF.  A third Dell quad core server is available to users who wish to do their own docking with supervision by Dr. Ken Satyshur. Other docking and display programs are also provided by SMSSF such as EPOS docking pocket identifier, FlexX, Grid docking, Pymol and ADT visualization software. For information contact Dr. Ken Satyshur at satyshur@wisc.edu.