Postdocs in Computational Biology

Bruce Randall Donald brd at
Fri Nov 30 01:54:37 PST 2001

Dartmouth College
Department of Computer Science (12/1/01)

Postdoctoral Research Associates in Computer Science: 

We have received two new NSF grants for research in Computational
Biology and Chemistry. We are looking for persons with a doctorate in
computer science to conduct focused research in computational biology,
specifically, on computational structural biology and computer-aided
drug design. Applications should be sent to Professor Bruce R. Donald.
For application instructions, more on this position, our research, job
placement for Donald Lab alumni, and life at Dartmouth, please see:

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. Our 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. Conversely, the algorithms and computational tools we develop
will be useful to the structural biology community, for studies of
protein-ligand binding and protein redesign. For example, we will
develop new techniques for computer-assisted drug design, including
algorithms for docking flexible ligands to flexible active sites. Our
web page and papers (see URL above) overview these projects, and
survey some of the algorithmic and computational challenges.

You will be working with a team of computer scientists, structural
biologists, protein chemists, biochemists, and biologists to advance
the state of the art in computational techniques for structural
biology and structure-based drug design. While the work has a strong
theoretical component, it will also require programming and system
building, experimental (computational) work, and the ability and
desire to work closely with biologists and chemists. A background in
geometric algorithms, rational drug design, molecular modeling,
docking, structural biology, robotics, or protein folding is a
definite plus.

Bruce Randall Donald
Professor of Computer Science
Adjunct Professor of Chemistry
6211 Sudikoff Laboratory, Rm. 113
Department of Computer Science
Hanover, NH 03755-3510


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