COLLOQUIUM ON COMPUTATIONAL BIOMOLECULAR SCIENCE

NATIONAL ACADEMY OF SCIENCES
WASHINGTON, D.C.
1998



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Colloquium on Computational Biomolecular Science COLLOQUIUM ON COMPUTATIONAL BIOMOLECULAR SCIENCE NATIONAL ACADEMY OF SCIENCES WASHINGTON, D.C. 1998

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Colloquium on Computational Biomolecular Science 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).

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Colloquium on Computational Biomolecular Science 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

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Colloquium on Computational Biomolecular Science 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

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Colloquium on Computational Biomolecular Science 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

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Colloquium on Computational Biomolecular Science 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.

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Colloquium on Computational Biomolecular Science 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