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| About Woody Sherman (Schrodinger) |
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Woody Sherman received his BS in Physical Chemistry from the University of California at Santa Barbara where he studied the non-linear optical properties of organic polymers through quantum mechanics calculations. He then went to MIT for his doctoral work with Prof. Bruce Tidor. The focus of his PhD dissertation was on understanding the interplay between ligand binding affinity and specificity using a novel methodology based on charge optimization in the continuum electrostatics framework. During his PhD work he took an internship with Biogen in Cambridge where he applied the charge optimization and ligand design methodology to antibody/antigen binding. He joined the Applications Science group at Schrodinger in 2004 where he worked on research projects, both with customers and internally, such as the Schrodinger Induced-Fit Docking methodology. He is currently the Director of Applications Science at Schrodinger and continues to develop new methods and applications for ligand- and structure-based drug design.
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Using fragments to couple ligand- and structure-based approaches.
Woody Sherman, Schrodinger
We have developed a method to generate structure-based pharmacophore hypotheses derived from the results of fragment docking. The quality of the results depends heavily on the ability of docking algorithm to accurately dock and score small fragments within the binding pocket. We first show that Glide XP is able to accurately dock and score fragments. We then describe the methodology used to generate chemically meaningful structure-based pharmacophore hypotheses that can be used in database searching. Results from database enrichment screens will be shown where good enrichments are obtained with the structure-based pharmacophore hypotheses and novel compounds are proposed based on the database screens.
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