We have been DOCKing combinatorial libraries to potential protein targets to determine the optimal library for a given target as well as alternative targets for a given library. For proof-of-concept, we are applying this approach to the serine, cysteine, and aspartyl proteases. The initial goal is to reproduce known subsite side chain specificities for the proteases, especially that of the S1 pocket of serine proteases. In addition, the subsites of the proteases have been characterized with a surface normal vector representation and used to rank scaffold orientations. Molecular surfaces calculated using the dms program and visualized using MidasPlus are key in this effort. In the future, we will address whether family-specific or member-specific subsite representations are useful for library enrichment.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR001081-23
Application #
6347900
Study Section
Project Start
2000-07-01
Project End
2001-06-30
Budget Start
1998-10-01
Budget End
1999-09-30
Support Year
23
Fiscal Year
2000
Total Cost
$136
Indirect Cost
Name
University of California San Francisco
Department
Type
DUNS #
073133571
City
San Francisco
State
CA
Country
United States
Zip Code
94143
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