NC State University

Department of Computer Science Colloquia 2001-2002

A telecast from UNC as part of
Triangle Computer Science Distinguished Lecturer Series

Date:   Monday, February 18, 2002
Time:   4:00 PM (talk telecast)
Place:   Parks Shop, Studio 1, NCSU Historical Campus (click for courtesy parking request)

Speaker:  Bruce Randall Donald , Computer Science & Chemistry, Dartmouth College

Algorithmic Challenges in Structural Molecular Biology

Abstract:   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. Among these problems are: identifying the low-energy conformations of molecules, interpreting protein NMR (nuclear magnetic resonance) and X-ray data, inferring constraints on the shape of active drug molecules based on measurements of activity of related drug molecules, and docking candidate drug molecules to known protein targets.

In the post-genomic era, key problems in molecular biology center on the determination and exploitation of three-dimensional protein structure and function. For example, modern drug design techniques use protein structure to understand how a drug can bind to an enzyme and inhibit its function. Structural proteomics will require high-throughput experimental techniques, coupled with sophisticated computer algorithms for data analysis and experiment planning. My lab is working in several areas, including: (1) data-directed computational protocols for high-throughput protein structure determination with nuclear magnetic resonance spectroscopy, and (2) experiment planning and data interpretation algorithms in structural mass spectrometry for protein complex binding-mode identification, and (3) reprogramming enzyme specificity, towards combinatorial biosynthesis for small-molecule diversity. In each area, computational techniques are central, and the applications present intriguing problems to computer scientists who design algorithms and implement systems. I'll overview these projects, and survey some of the algorithmic and computational challenges.

Short Bio:   Bruce Randall Donald has been conducting research and development in Computer Science and Engineering for over 20 years. He has worked in several research areas, including Robotics, Microelectromechanical Systems (MEMS), Computational Biology, Graphics, and Geometric Algorithms. Donald has been at Yale, Harvard, MIT, Cornell, Stanford, Interval Research Corporation, and Dartmouth.

Bruce Donald graduated summa cum laude from Yale University in 1980. From 1978-84, he was a Research Analyst in the Laboratory for Computer Graphics and Spatial Analysis in the Harvard University Graduate School of Design, where he worked on Geographical Information Systems (GIS) and computer-aided architectural design. In 1982, he began working under the direction of Professor Tomas Lozano-Perez at the MIT Artificial Intelligence Laboratory, and received the SM degree in EECS and a Ph.D. degree in CS from MIT in 1987.

Donald then joined the faculty of the Cornell University Computer Science Department, where he rose through the ranks to tenure in in 1993. At Cornell, he held a joint appointment in Applied Mathematics. Donald co-founded the Cornell Robotics and Vision Laboratory. He received a National Science Foundation Presidential Young Investigator Award in 1989, and an NSF Challenges in Computer and Information Science and Engineering (CISE) grant in 1997. After a decade on the Cornell faculty, Donald joined the Computer Science Department at Dartmouth in 1997, where he is currently Professor of Computer Science, and Adjunct Professor of Chemistry.

Donald has written four books and numerous scientific papers on robotics, physical geometric algorithms, graphics, MEMS, and computational biology, and was a visiting professor at Stanford University (1994-96). From 1995-97, Donald worked at Interval Research Corporation (in Palo Alto), where he was co-inventor of Embedded Constraint Graphics (ECG). Donald was conference chair of the International Workshop on Algorithmic Foundations of Robotics (WAFR), 2000. His latest research interest is in computational structural biology and drug design. Donald founded the Dartmouth Medical School/Dartmouth College M.D.-Ph.D. Program in Computational Biology, and is a member of the Dartmouth Center for Structural Biology and Computational Chemistry. He serves on the Scientific Advisory Board of Carta Proteomics, Inc. Dr. Donald was awarded a Guggenheim Fellowship in 2001, for his work on structural proteomics (algorithms for high-throughput structural molecular biology). He was a Visiting Scientist at the MIT Artificial Intelligence Lab and Department of EECS (2000-2001).

Former Students and PostDocs from Donald's lab include: Chris Bailey-Kellogg (Purdue), Karl Bohringer (University of Washington), Amy Briggs (Middlebury), Russell Brown (Sandia), Jim Jennings (Tulane), Dinesh Pai (UBC), Jonathan Rees (MIT/Sussex), Daniela Rus (Dartmouth), and Pat Xavier (Sandia).

Host:   J. Snoeyink , Computer Science, UNC

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