My group focuses on structure-based ligand design methods. We are interested in computer graphics routines to display structures and information, refinement procedures, interactive energy minimization with state-of-the-art potential functions, and drug design tools such as DOCK and COMBIDOCK. We can now couple organic synthesis (UC_SELECT, UC_REACT) with computational searching. These programs, in a WEB-based wrapper, use organic transformations to generate a large family of products from specified starting points. The reagents and/or resulting compounds can then be screened using our CombiDOCK software. The DOCK suite of programs has wide-ranging applications to enzyme systems, nucleic acids, and, in general, problems involving molecular recognition.The current version of the program uses the AMBER intermolecular potential functions to evaluate proposed binding geometries. DOCK was developed to propose novel lead compounds. It has been successful in this goal in a wide variety of systems, including recent, unpublished work identifying novel inhibitors of the HIV reverse transcriptase and HIV integrase.
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