Docking and scoring: Improvements in screening enrichment and docking accuracy


Ajay Jain, Cancer Research Institute, Cancer Research Institute, University of California, San Francisco, Box 0128, San Francisco, CA 94143-0128
Docking algorithms seek to extremize the value of a scoring function by finding the optimal conformation and alignment (pose) of a ligand relative to a protein binding site. The Surflex docking method employs an empirically constructed scoring function and a search methodology that makes use of molecular similarity based pose generation. Comparative results will be presented on both docking accuracy (geometric agreement with crystallographic experiment) and screening enrichment (ability to distinguish true positives from false positives). Particular emphasis will be on screening efficiency and methods to improve scoring functions by explicit training using putative false positives. Performance of Surflex v1.21 is competitive with many popular docking methods for docking accuracy and appears to be significantly better for screening enrichment.

Docking and Scoring
9:00 AM-12:20 PM, Sunday, August 22, 2004 Pennsylvania Convention Center -- 109B, Oral

Division of Computers in Chemistry

The 228th ACS National Meeting, in Philadelphia, PA, August 22-26, 2004