 Hampden-Sydney Student Research Published in ACS Journal
Andy Surface, a junior chemistry major at Hampden-Sydney College, has been published as
second author in the American Chemical Society's Journal of Medicinal Chemistry
for his contributing work to a project based
out of Virginia Commonwealth University's Medicinal Chemistry Department (Institute of Structural
Biology and Drug Development). Over this past summer, through the Bioinformatics and
Bioengineering Summer Institute's grant from NIH/NSF, Andy worked with Professor Glen Kellogg
(VCU) and Alessio Amadasi (University of Parma) on a project that involved building a mathematical
model to predict water behavior in protein active sites.
Andy's contribution to the work was both mathematical and chemical. His portion of the project
involved analyzing the data results from computational assays done on PDB protein structures
analyzing water retention and affinity. He invented and built a heuristic, double-probability statistical
system that used weighted averages to predict water affinity to as high as 92% in high-resolution x-ray
structures (previous attempts at this had been in the 70-80% range, using much more complicated
systems). The simple mathematical system, based on Dr. Glen Kellogg's HINT and RANK models, was
then programmed as a fast-scanning algorithm that could target water molecules in proteins in the
molecular modeling program, Sybyl, to help medicinal chemists around the world target waters that
may be an issue in ligand binding.
Much of Andy's ability to do this work he attributes to the Hampden-Sydney Chemistry Department's
excellent program. "They train you to think about real-world problems, not just to know
things," Andy said. His two primary supporting professors, Dr. William
Anderson and Dr. Paul Mueller, along with Dr. Herbert Sipe, Andy's advisor, helped
him get into the BBSI program, and they have been the supporting
professors this academic year as Andy continues to carry on further research, some of which he will present to the BBSI this coming
summer.
His article, Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites, was just released on January 31, 2008, on the ACS's Journal of Medicinal Chemistry
website, and will be released in print in the next Journal of Medicinal Chemistry issue.
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