Some of the most challenging and influential opportunities for Physical Geometric Algorithms (PGA) arise in developing and applying information technology to understand the molecular machinery of the cell. Our recent work (and work by others) shows that many PGA techniques may be fruitfully applied to the challenges of computational molecular biology. PGA research may lead to computer systems and algorithms that are useful in structural molecular biology, proteomics, and rational drug design.
Concomitantly, a wealth of interesting computational problems arise in proposed methods for discovering new pharmaceuticals. In this talk, I’ll discuss some recent results from my lab, including new algorithms for interpreting X-ray crystallography and NMR (nuclear magnetic resonance) data, disease classification using mass spectrometry of human serum, and protein redesign. Our algorithms have recently been used, respectively, to reveal the enzymatic architecture of organisms high on the CDC bioterrorism watch-list, for probabilistic cancer classification from human peripheral blood, and to redesign an antibiotic-producing enzyme to bind a novel substrate. I’ll overview these projects, and survey some of the algorithmic and computational challenges.
Bruce Donald is the Joan P. and Edward J. Foley Jr 1933 Professor in the Computer Science Department at Dartmouth. He holds a joint appointment in the Department of Chemistry and the Department of Biological Sciences. From 1987-1998, Donald was a professor in the the Cornell University Computer Science Department, with a joint appointment in Applied Mathematics. He received a B.A. from Yale University, and a Ph.D. from MIT. Donald has worked in research, visiting, and faculty positions at Harvard, Stanford, Interval Research Corporation, and MIT.
Donald has been a National Science Foundation Presidential Young Investigator. He has worked in in several research areas, including Robotics, Microelectromechanical Systems (MEMS), Computational Biology, Graphics, and Geometric Algorithms. Donald’s latest research interest is in computational structural biology and drug design. He was awarded a Guggenheim Fellowship for his work on algorithms for structural proteomics. Research in the Donald laboratory is funded by the National Institutes of Health under the auspices of the National Institute of General Medical Sciences Protein Structure Initiative.