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Molecular Modeling and Drug Docking Hands-on Course


Digital Media Center Teaching Lab,

Biochemical Sciences Building

420 Henry Mall


For more information:

What:  'Hands on' 8 week course on molecular modeling with an emphasis on drug design.

Who:   Any grad student or staff of the UW

When: Spring Semester


The Small Molecule Screening and Synthesis Facility (SMSSF) in the UW Comprehensive Cancer Center (School of Medicine and Public Health) uses high-throughput screening robotics to screen database of chemicals in chemical assays for small molecule interactions with drug targets.


To assist in understanding how these small molecules interact with their targets, the SMSSF provides molecular modeling services, including in-silico drug docking services. The SMSSF also provides an opportunity for the community to learn how to model these drugs in their targets.


This course will cover the basics of protein and small molecule modeling using the commercial software Sybyl from Tripos. Then several docking programs, such as SurFlex, DOCK, and Autodock4, will be examined with real examples form the literature.


Held in the Digital Media Center teaching lab in the very new Biochemistry Building, each student will be running Sybyl on a Linux server thru a Macintosh interface.



The course has been taught the last five years by Dr. Ken Satyshur, from the SMSSF who has more than 25 years experience with molecular modeling. Contact Dr. Ken Satyshur if you wish to participate. 


New this year: How to use the electron density fitting program Coot to examine published X-ray crystal structures.

Learn more about the Small Molecule Screening and Synthesis Facility.



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