National Academies Press: OpenBook
Suggested Citation:"Front Matter." National Academy of Sciences. 1998. (NAS Colloquium) Computational Biomolecular Science. Washington, DC: The National Academies Press. doi: 10.17226/6239.
×

COLLOQUIUM ON COMPUTATIONAL BIOMOLECULAR SCIENCE

NATIONAL ACADEMY OF SCIENCES
WASHINGTON, D.C.
1998

Suggested Citation:"Front Matter." National Academy of Sciences. 1998. (NAS Colloquium) Computational Biomolecular Science. Washington, DC: The National Academies Press. doi: 10.17226/6239.
×

NATIONAL ACADEMY OF SCIENCES

Colloquium Series

In 1991, the National Academy of Sciences inaugurated a series of scientific colloquia, five or six of which are scheduled each year under the guidance of the NAS Council’s Committee on Scientific Programs. Each colloquium addresses a scientific topic of broad and topical interest, cutting across two or more of the traditional disciplines. Typically two days long, colloquia are international in scope and bring together leading scientists in the field. Papers from colloquia are published in Proceedings of the National Academy of Sciences (PNAS).

Suggested Citation:"Front Matter." National Academy of Sciences. 1998. (NAS Colloquium) Computational Biomolecular Science. Washington, DC: The National Academies Press. doi: 10.17226/6239.
×

COMPLETED NAS COLLOQUIA

(1991 TO PRESENT)

Industrial Ecology

May 20–21, 1991; Washington, D.C.

Organizer: C.Kumar N.Patel

Proceedings: February 4, 1992

Images of Science: Science of Images

January 13–14, 1992; Washington, D.C.

Organizer: Albert Crewe

Proceedings: November 3, 1993

Physical Cosmology

March 27–29, 1992; Irvine, California

Organizer: David Schramm

Proceedings: June 3, 1993

Molecular Recognition

September 10–11, 1992; Washington, D.C.

Organizer: Ronald Breslow

Proceedings: February 16, 1993

Human-Machine Communication by Voice

February 8–9, 1993: Irvine, California

Organizer: Lawrence Rabiner

Proceedings: October 24, 1995

Changing Human Ecology and Behavior: Effects on Infectious Diseases

September 27–28, 1993; Washington, D.C.

Organizer: Bernard Roizman

Proceedings: March 29, 1994

The Tempo and Mode of Evolution

January 27–29, 1994; Irvine, California

Organizers: Francisco Ayala, Walter Fitch

Proceedings: July 19, 1994

Chemical Ecology: The Chemistry of Biotic Interaction

March 25–26, 1994; Washington, D.C.

Organizers: Thomas Eisner, Jerrold Meinwald

Proceedings: January 3, 1995

Physics: The Opening to Complexity

June 25–27, 1994; Irvine, California

Organizer: Philip Anderson

Proceedings: July 18, 1995

Self Defense by Plants: Induction and Signaling Pathways

September 15–17, 1994; Irvine, California

Organizers: André Jagendorf, Clarence Ryan

Proceedings: May 9, 1995

Earthquake Prediction

February 10–11, 1995; Irvine, California

Organizer: Leon Knopoff

Proceedings: April 30, 1996

Quasars and Active Galaxies: High Resolution Radio Imaging

March 24–25, 1995; Irvine, California

Organizers: Marshall Cohen, Kenneth Kellerman

Proceedings: December 5, 1995

Vision: From Photon to Perception

May 21–22, 1995; Irvine, California

Organizers: John Dowling, Lubert Stryer, and Torsten Wiesel

Proceedings: January 23, 1996

Science, Technology, and the Economy

October 20–22, 1995; Irvine, California

Organizers: James Heckman, Ariel Pakes, and Kenneth Sokoloff

Proceedings: November 12, 1996

Developmental Biology of Transcription Control

October 25–28, 1995; Irvine, California

Organizers: Roy Britten, Eric Davidson, and Gary Felsenfeld

Proceedings: September 3, 1996

Carbon Dioxide and Climate Change

November 13–15, 1995; Irvine, California

Organizer: Charles Keeling

Proceedings: August 5, 1997

Memory: Recording Experience in Cells and Circuits

February 17–20, 1996; Irvine, California

Organizer: Patricia Goldman-Rakic

Proceedings: November 26, 1996

Suggested Citation:"Front Matter." National Academy of Sciences. 1998. (NAS Colloquium) Computational Biomolecular Science. Washington, DC: The National Academies Press. doi: 10.17226/6239.
×

COMPLETED NAS COLLOQUIA

Elliptic Curves and Modular Forms

March 15–17, 1996; Washington, D.C.

Organizers: Barry Mazur, Karl Rubin

Proceedings: October 14, 1997

Symmetries Throughout the Sciences

May 10–12, 1996; Irvine, California

Organizer: Ernest Henley

Proceedings: December 15, 1996

Genetic Engineering of Viruses and Viral Vectors

June 9–11, 1996; Irvine, California

Organizers: Peter Palese, Bernard Roizman

Proceedings: October 15, 1996

Genetics and the Origin of Species

January 30-February 1, 1997; Irvine, California

Organizers: Francisco Ayala, Walter Fitch

Proceedings: July 22, 1997

The Age of the Universe: Dark Matter and Structure Formation

March 21–23, 1997; Irvine, California

Organizers: David Schramm, P.J.E.Peebles

Proceedings: January 6, 1998

Neuroimaging and Human Brain Function

May 29–31, 1997; Irvine, California

Organizers: Michael Posner, Marcus Raichle

Proceedings: February 3, 1998

Protecting Our Food Supply: The Value of Plant Genome Initiatives

June 2–4, 1997; Irvine, California

Organizers: Michael Freeling, Ronald Phillips, John Axtell

Proceedings: March 5, 1998

Computational Biomolecular Science

September 11–14, 1997; Irvine, California

Organizers: Peter G.Wolynes, Russell Doolittle, J.A.McCammon

Proceedings: May 26, 1998

A Library Approach to Chemistry

October 19–21, 1997; Irvine, California

Organizer: Peter Schultz, Jonathan Ellman

Suggested Citation:"Front Matter." National Academy of Sciences. 1998. (NAS Colloquium) Computational Biomolecular Science. Washington, DC: The National Academies Press. doi: 10.17226/6239.
×

PROGRAM

Computational Biomolecular Science

Thursday, September 11, 1997

Registration and Welcome Reception

Friday, September 12, 1997

Session I

8:45 AM-12:30 PM

Introduction, Peter Wolynes.

Measuring genome evolution. Peer Bork (EMBL, Heidelberg).

Determining biological function from sequence: Building highly specific sequence motifs for genome analysis. Douglas Brutlag (Stanford).

Experimental studies of protein folding dynamics. William Eaton (NIH).

Coupling the folding of homologous proteins. Ron Elber (Hebrew University).

Chair, Russell Doolittle

Session II

2:00 PM-5:30 PM

Photoactive yellow protein: Prototype for the PAS domains of sensors and clocks. Elizabeth Getzoff (Scripps Research Institute).

Inhomogeneities in genomic sequence composition. Philip Green (Univ. Washington).

New refinement methods for NOE-distance based NMR structure. Angela Gronenborn (NIH).

Estimation of evolutionary distances between DNA sequences. Wen-Hsiung Li (Univ. Texas, Houston).

Comments by Roy Britten

After-dinner Lecture. From slide rule to super computer. Hans Frauenfelder (Los Alamos).

Chair, Andrew McCammon

Saturday, September 13, 1997

Session III

9:00 AM-12:30 PM

Comparing sequence comparison with structure comparison. Michael Levitt (Stanford).

Structural classification of proteins and its evolutionary implications. Alexey Murzin (MRC, Cambridge).

Exploring the protein folding funnel landscape-connection to fast folding experiments. Jose Onuchic (UCSD).

Bridged bimetallic enzymes: A challenge for computational chemistry. Gregory Petsko (Brandeis).

Chair, Andrew McCammon

Session IV

2:00 PM-5:30 PM

Sequence determinants of protein folding and stability. Robert Sauer (MIT).

The evolution of efficient light harvesting in photosynthesis-one goal, many solutions. Klaus Schulten (Illinois).

Electrostatic steering and ionic tethering in simulations of protein-ligand interactions. Rebecca Wade (EMBL, Heidelberg).

Computer simulation of enzymatic reactions and other biological process; finding out what was optimized by evolution. Arieh Warshel (USC).

After-dinner Lecture. Applications of computers in structural biology. Harold Scheraga (Cornell).

Chair, Peter Wolynes

Suggested Citation:"Front Matter." National Academy of Sciences. 1998. (NAS Colloquium) Computational Biomolecular Science. Washington, DC: The National Academies Press. doi: 10.17226/6239.
×

LIST OF ATTENDEES

Computational Biomolecular Science

Robert K.Adair, Yale University

Paul A.Bash, Argone National Laboratory

R.L.Bernstein, San Francisco State University

Paul Beroza, CombiChem Inc.

Peer Bork, European Molecular Biology Laboratory

David A.Brant, University of California

Roy J.Britten, California Institute of Technology

Thomas C.Bruice, University of California, Santa Barbara

Douglas Brutlag, Stanford University Medical School

Aloke Chatterjee. Lawrence Berkeley National Laboratory

Jiangang Chen, University of California, Los Angeles

Margaret S.Cheung, University of California, San Diego

Julian D.Cole, Rensselaer Polytechnic Institute

Kumari Devulapalle, University of Southern California, School of Dentistry

Russel F.Doolittle, University of California, San Diego

William Eaton, National Institutes of Health Ron Elber, Hebrew University

Adrien Elcock, University of California, San Diego

Hans Frauenfelder, Los Alamos National Laboratory

Anthony Gamst, University of California, San Diego

Robert Gerber, University of California, Irvine

Elizabeth D.Getzoff, Scripps Research Institute

Raveh Gill-More, Compugen Ltd.

Adam Godzik, The Scripps Research Institute

Jill E.Gready, Australian National University

Phillip Green, University of Washington

Angela M.Gronenborn, National Institutes of Health

William Grundy, University of California. San Diego

Volkhard Helms, University of California San Diego

Dennis Kibler, University of California, Irvine

Robert Konecny, The Scripps Research Institute

Kristin Korethe, Smith Kline Beecham

Leslie A.Kuhn, Michigan State University

Donald Kyle, Scios Inc.

Peter W.Langhoff, San Diego Supercomputer Center

Michael Levitt, Stanford University, School of Medicine

Jian Li, The Scripps Research Institute

Wen-Hsiung Li, University of Texas

E.N.Lightfoot, University of Wisconsin

Jennifer H.Y.Liu, University of California

Hartmut Luecke, University of California, Irvine

Jia Luo, University of California, Santa Barbara

Zaida Luthey-Schultem, University of Ilinois

Jeffry D.Madura, University of South Alabama

J.Andrew McCammon, University of California, San Diego

Gregory Mooser, University of Southern California, School of Dentistry

Victor Munoz, National Institutes of Health

Alexey G.Murzin, Centre for Protein Engineering

Craig Nevill-Manning, Stanford University

Louis Noodleman, The Scripps Research Institute

Hugh Nymeyer, University of California, San Diego

Jose N.Onuchic, University of California, San Diego

Jean-Luc Pellequer, The Scripps Research Institute

Gregory A.Petsko, Brandeis University

Mike Potter, University of California, San Diego

Vijay S.Reddy, The Scripps Research Institute

Carolina M.Reyes, University of California, San Francisco

Roy Riblet, Medical Biology Institute

Andrey Rzhetsky, Columbia University

Suzanne B.Sandmeyer, University of California, Irvine

Robert Sauer, Massachusetts Institute of Technology

Harold Scheraga, Cornell University

Rebecca K.Schmidt, Australian National University

Klaus Schulten, University of Illinois

Soheil Shams, BioDiscovery

Sylvia Spengler, Lawrence Berkeley National Laboratory

Tim Springer, Center for Blood Research

T.P.Straatsma, Pacific Northwest National Laboratory

Ivan Suthsland, Sun Microsystems Laboratories

Mounir Tarek, National Institute of Standards and Technology

Douglas Tobias, University of California, Irvine

Chandra S.Verma, University of York

Rebecca Wade, European Molecular Biology Laboratory

Frederic Y.M.Wan, University of California, Irvine

Arieh Warshel, University of Southern California

Stephen H.White, University of California, Irvine

Peter Wolynes, National Institutes of Health

Willy Wriggers, University of Illinois at Urbana-Champaign

William V.Wright University of North Carolina

Thomas Wu, Stanford University

Qiang Zhenq, Scios Inc.

Suggested Citation:"Front Matter." National Academy of Sciences. 1998. (NAS Colloquium) Computational Biomolecular Science. Washington, DC: The National Academies Press. doi: 10.17226/6239.
×

PROCEEDINGS

OF THE

NATIONAL ACADEMY OF SCIENCES

OF THE UNITED STATES OF AMERICA

Table of Contents

Papers from a National Academy of Sciences Colloquium on Computational Biomolecular Science

 

 

Computational biomolecular science
Peter G.Wolynes

 

5848

 

 

Measuring genome evolution
Martijn A.Huynen and Peer Bork

 

5849–5856

 

 

SMART, a simple modular architecture research tool: Identification of signaling domains
Jörg Schultz, Frank Milpetz, Peer Bork, and Chris P.Ponting

 

5857–5864

 

 

Highly specific protein sequence motifs for genome analysis
Craig G.Nevill-Manning, Thomas D.Wu, and Douglas L.Brutlag

 

5865–5871

 

 

A statistical mechanical model for β-hairpin kinetics
Victor Munoz, Eric R.Henry, James Hofrichter, and William A.Eaton

 

5872–5879

 

 

Coupling the folding of homologous proteins
Chen Keasar, Dror Tobi, Ron Elber, and Jeff Skolnick

 

5880–5883

 

 

Photoactive yellow protein: A structural prototype for the three-dimensional fold of the PAS domain superfamily
Jean-Luc Pellequer. Karen A.Wager-Smith, Steve A.Kay, and Elizabeth D.Getzoff

 

5884–5890

 

 

New methods of structure refinement for macromolecular structure determination by NMR
G.Marius Clore and Angela M.Gronenborn

 

5891–5898

 

 

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution
Xun Gu and Wen-Hsiung Li

 

5899–5905

 

 

Precise sequence complementarity between yeast chromosome ends and two classes of just-subtelomeric sequences
Roy J.Britten

 

5906–5912

 

 

A unified statistical framework for sequence comparison and structure comparison
Michael Levitt and Mark Gerstein

 

5913–5920

 

 

Folding funnels and frustration in off-lattice minimalist protein landscapes
Hugh Nymeyer, Angel E.García, and José Nelson Onuchic

 

5921–5928

 

 

Optimizing the stability of single-chain proteins by linker length and composition mutagenesis
Clifford R.Robinson and Robert T.Sauer

 

5929–5934

 

 

Architecture and mechanism of the light-harvesting apparatus of purple bacteria
Xiche Hu, Ana Damjanović, Thorsten Ritz, and Klaus Schulten

 

5935–5941

 

 

Electrostatic steering and ionic tethering in enzyme-ligand binding: Insights from simulations
Rebecca C.Wade, Razif R.Gabdoulline, Susanna K.Lüdemann, and Valère Lounnas

 

5942–5949

 

 

Computer simulations of enzyme catalysis: Finding out what has been optimized by evolution
Arieh Warshel and Jan Florián

 

5950–5955

Suggested Citation:"Front Matter." National Academy of Sciences. 1998. (NAS Colloquium) Computational Biomolecular Science. Washington, DC: The National Academies Press. doi: 10.17226/6239.
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