* Elected Member, National Academy of Sciences of the USA (2011)
* American Chemical Society (ACS) National Award for Computers in Chemical and Pharmaceutical Research (2008)
* Elected Fellow, American Academy of Arts and Sciences (2006)
* UCSD SPPS Associated Students Teaching Award (2003)
* UC Chancellor's Associates Award for Research (2002)
* Appointed Investigator, Howard Hughes Medical Institute (2000–present)
* Joseph E. Mayer Chair of Theoretical Chemistry, UC San Diego (1995-)
* Smithsonian Award for Breakthrough Computational Science (1995)
* Cray Research Information Technology Leadership Award (1995)
* George Hitchings Award for Innovative Methods in Drug Design, Burroughs Wellcome Fund (1987–1992)
* Dreyfus Teacher-Scholar Award (1982–87)
* NIH Research Career Development Award (1980–85)