Enhanced ligand docking and scoring with LigandFit


C. M. Venkatachalam, Jeff Jiang, André Krammer, and Marvin Waldman. Accelrys, 9685 Scranton Road, San Diego, CA 92121
We present recent improvements to the LIGANDFIT program including algorithmic enhancements to improve positional and orientational sampling of the ligand and better selection of poses retained for scoring. Improved sampling is achieved by employing “site partitioning” where the binding site is further partitioned into smaller sites of various sizes and the ligand aligned to various partitioned sites by shape comparison. This procedure has been recently further refined by considering sites obtained by fusing various adjoining sites. In cases where the defined binding site is much larger than the size of the candidate ligand, the site partitioning technique significantly improves the quality of the docking. Results obtained with various Protein-Ligand complexes using this improved sampling will be presented. A technique for retaining poses that improves the overall diversity of the pose list will be discussed. Finally, ongoing work in the area of scoring function development will also be presented.

Docking and Scoring
9:00 AM-12:20 PM, Monday, August 23, 2004 Pennsylvania Convention Center -- 109A, Oral

Division of Computers in Chemistry

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