American Family Children's Hospital

Modeling and Virtual Screening

Pymol image of the tgfbeta Smad3/Smad4 The Small Molecule Screening Facility (SMSF) provides clients with computational infrastructure, software and expertise for molecular modeling of small molecules bound to proteins of known structure and for virtual screening of millions of small molecules at defined pockets on proteins of known structure using in silico docking methods. 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 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 SMSF. 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 SMSF such as EPOS docking pocket identifier, Pymol, and AutoDockTools visualization software.


For information contact Dr. Ken Satyshur.  


Hands-on Course in Molecular Modeling and Drug Docking


The SMSF also sponsors a “hands on” 8-week course on molecular modeling with an emphasis on drug design called “Molecular Modeling and Drug Docking” for the UW community to learn how to model the drugs in their targets. The course covers the basics of protein and small molecule modeling using the commercial software Sybyl from Tripos. Several docking programs, such as SurFlex, DOCK and Autodock4, are examined with real examples from the literature. 


The course is held in the Digital Media Center teaching lab in the Biochemical Sciences Building, 420 Henry Mall. Each student runs Sybyl on a Linux server thru a Macintosh interface. There is no UW credit for this course. The course has been taught the last five years by Dr. Ken Satyshur from the SMSF during the Spring semester.


Find out more about the Molecular Modeling and Drug Docking Hands-on Course