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IMA-MSI Workshop
Mathematical and Computational Issues in Drug Design
April 7-11, 1997


Mathematics of High Performance Computing
Parallel Computational Mechanics

Organizers:

Jeff Blaney (Chiron)
Richard Dammkoehler (Washington University)
Tony Hopfinger (Univ. of Illinois-Chicago)
Jeffrey Howe (Upjohn Company)
Donald Truhlar (Minnesota Supercomputer Institute)

Sponsored jointly with the Minnesota Supercomputer Institute

 

Drug research and discovey are of critical importance in human health care and are becoming increasingly expensive, while the need for new drugs is also increasing. Computational approaches for drug discovery and optimization have proven successful in many recent research programs. These methods have grown in their effectiveness not only because of improved understanding of the basic science -- the biological events and molecular interactions that define a target for therapeutic intervention -- but also because of advances in algorithms, representations and mathematical procedures for studying such processes.

This workshop will bring together top researchers in computer-aided drug discovery, computational chemistry, mathematics, and computer science to present state-of-the-art research in both the science and the underlying mathematics, and to identify new problems for possible collaborations. General subject areas of the workshop will include receptor-based applications such as binding energy approximations, molecular docking, and de novo design; non-receptor-based applications such as molecular similarity, confirmational analysis, and structural diversity; molecular dynamics simulations and protein folding simulations; plus related issues such as drug delivery modelling and scientific visualization. The workshop will also focus on the mathematical procedures and algorithms upon which the scientific applications are based. These include graph theory and topology, nonlinear multidimensional optimization, the processing and representation of information obtained from simulation studies, global optimization and search strategies, plus performance enhancement through parallel computing architectures. In addition to the oral presentations, the workshop will also include two panel discussions, one examining the most important current problems in drug design that may be computationally tractable, and the second on emerging areas of study in which improvements in scientific knowledge over the next few years may enable the fruitful application of computational methods. The overall goal of this workshop is to bring together scientists and mathematicians to examine the current state of this very broad and interdisciplinary field of research, and to identify the areas where cross-fertilization of ideas and collaborative research might most effectively advance the field.

Workshop Schedule

All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.

Text-only version of this schedule

SCHEDULE for MONDAY, APRIL 7
8:15 am Coffee Reception Room EE/CS 3-176
Morning - Session Chair:   Donald G. Truhlar, University of Minnesota
9:00am Garland Marshall,
Washington University
Prediction of Affinities of Molecular Complexes: A Hybrid Approach
10:00 am Break Reception Room EE/CS 3-176
10:30 am Peter Willett,
University of Sheffield
Matching Chemical and Biological Structures Using Graph-Theoretical Techniques
11:30 am Lunch  
Afternoon - Session Chair:   Jeffrey Howe, Pharmacia & Upjohn
1:15 pm W. Graham Richards,
Oxford University
Molecular Similarity
2:15 pm Break Reception Room EE/CS 3-176
2:30 pm Panel Discussion, Chaired by Jeff Howe and Tony Hopfinger

Panelists:
Dave Doherty, MSI
Bill Dunn, Univ. of Ill., Chicago
W. Graham Richards, Oxford Univ.
Doug Rohrer, Pharmacia/Upjohn

What are the most important problems in drug design that may be computationally tractable?
4:00 pm IMA Tea Vincent Hall 502 (IMA Lounge)
SCHEDULE for TUESDAY, APRIL 8
8:45 am Coffee Reception Room EE/CS 3-176
Morning - Session Chair:   Rich Dammkoehler, Washington University
9:00 am Christopher Cramer,
University of Minnesota
Solvation Effects and Their Impact on Drug Design
10:15 am Break Reception Room EE/CS 3-176
10:45 am Jeff Blaney,
Chiron
Combinatorial Chemistry and Molecular Diversity
11:45 am Lunch  
Afternoon - Session Chair:   Jeff Blaney, Chiron Corporation
2:00 pm Colin McMartin,
Thistlesoft
Interactive Molecular Design using Binding Sites and Pharmacophores with Reference to the Potency Prediction Problem
3:00 pm Break Reception Room EE/CS 3-176
3:30 pm Regine Bohacek,
Ariad Pharmaceuticals
Application of the GrowMol Computer Program to the Aspartic Acid Pepsin: Results of the Design and Synthesis of a Novel Inhibitor
SCHEDULE for WEDNESDAY, APRIL 9
8:45 am Coffee Reception Room EE/CS 3-176
Morning - Session Chair:   Tim Havel, Harvard Medical School
9:15am Ken Dill,
University of California at San Francisco
Two Problems in Drug Design: Additivity Principles and Conformational Search Strategies
10:15 am Break Reception Room EE/CS 3-176
10:45 am Dennis Sprous,
Wesleyan University
Molecular Dynamics Information Extraction
11:45 am Lunch  
Afternoon - Session Chair:   Tony Hopfinger, University of Illinois at Chicago
2:00 pm Thomas A. Darden,
National Inst. of Environmental Health Science
Molecular Dynamics Simulations Using Fast Ewald Summation
3:00 pm Break Reception Room EE/CS 3-176
3:30 pm Panel Discussion, Chaired by Jeff Blaney

Panelists:
Gordon Crippen, Univ. of Michigan
Simon Kearsley, Merck
Garland Marshall, Washington Univ
Phil Portoghese, Univ. of Minnesota

What are the new problems that should be addressed in the next ten years?
SCHEDULE for THURSDAY, APRIL 10
8:45 am Coffee Reception Room EE/CS 3-176
Morning - Session Chair:   Simon Kearsley, Merck Research
9:15 am Markus Wagener,
SmithKline Beecham
Applications of Neural Networks in Drug Design
10:15 am Break Reception Room EE/CS 3-176
10:45 am David Rogers,
Molecular Simulations Inc.
To Be Announced
11:45 am Lunch  
Afternoon - Session Chair:   Jeffrey Howe, Pharmacia & Upjohn
2:00 pm Brian T. Luke,
National Cancer Institute
Frederick Cancer Research Ctr.
Applications of Distributed Computing to Molecular Modeling and Drug Discovery
3:00 pm Break Reception Room EE/CS 3-176
3:30 pm Jason Rush,
University of Washington
Cell-based methods for sampling high-dimensional spaces
6:00 pm Reception Radisson Hotel Alumni Room, 2nd Floor
7:00 pm Banquet Radisson Hotel Alumni Room, 2nd Floor
After Dinner Ralph Hirschmann,
Univerity of Pennsylvania
Rational Drug Design and All That. An Evolutionary Process
SCHEDULE for FRIDAY, APRIL 11
8:30 am Coffee Reception Room EE/CS 3-176
Morning - Session Chair:   Tony Hopfinger, University of Illinois at Chicago
9:00 am Gordon Crippen,
University of Michigan
Deducing Objective Site Models by Mixed Integer Programming
10:00 am Hirofumi Doi,
Fujitsu Labs Ltd.
Finding New Function Sites of Proteins Based on Frequency Analysis of Oligopeptides in the Genome Data
10:30 am Break Reception Room EE/CS 3-176
11:00 am Michael Pique,
The Scripps Research Institute
Visualization and the Internet

 

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1996-1997 Mathematics in High Performance Computing

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