*  Fellow of the Biophysical Society, 2016
*  Gilda Loew Memorial Award of the International Society of Quantum Biology and Pharmacology (ISQBP), 2014
*  Hans Neurath Award - The Protein Society, 2012
* Top 100 Chemists of 2000-2010 as identified by Thomson Reuters, 2011
* Purdue University Chemistry Alumni of the Year, 2010
* North American Editor of the Journal of Computational Chemistry, 2004
* Fellow of the American Association for the Advancement of Science, 2002
*  Computerworld Smithsonian Award in Computational Science, 1997
* Alfred P. Sloan Foundation Fellow, 1992