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IMA Annual Program Year Workshop

Protein Folding

January 14-18, 2008
Organizers:
Ken A. Dill Pharmaceutical Chemistry, University of California
Sorin Istrail Computer Science, Brown University
Michael Levitt Structural Biology, Stanford University School of Medicine

Schedule Participants Program Application Feedback
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Abstracts and Talk Materials Dining Guide

Description:

Modern questions of biological science are becoming increasingly quantitative and microscopic, and increasingly approachable by physical models and computer simulations. This workshop is focused at the interface where molecular and cellular biology meet the mathematical and computational sciences. We will explore both principles and methodologies, particularly those that are rooted in physics and rigorous mathematics, in addition to applications to biological problems. Research topics will include the computational folding of proteins and other biomolecules, ligand docking, biological networks, heterogeneous dynamics, and complex systems. Speakers will be encouraged to present new work, and to identify important unsolved problems and opportunities at this interface.

Schedule
Monday | Tuesday | Wednesday | Thursday | Friday | 
  Monday, January 14
Morning Theme: Force fields & simulations
Afternoon Theme: Design, predictions, and optimization
8:15a-9:00a Registration and coffee   EE/CS 3-176
9:00a-9:15a Welcome to the IMA Douglas N. Arnold (University of Minnesota) EE/CS 3-180
9:15a-9:45a Assessing the performance of Poisson-Boltzmann continuum solvation models Nathan A. Baker (Washington University School of Medicine) EE/CS 3-180
9:50a-10:20a Simple models for simulating replica exchange simulations of protein folding and binding Ronald M. Levy (Rutgers University) EE/CS 3-180
10:25a-10:55a Alpha-helical topology and tertiary structure prediction of globular proteins Christodoulos A. Floudas (Princeton University) EE/CS 3-180
10:55a-11:40a Coffee   EE/CS 3-176
11:40a-12:10p Challenges in generation of conformational ensembles for peptides and small proteins Carlos L. Simmerling (SUNY) EE/CS 3-180
12:15p-12:30p What is a transition path? Robert D. Skeel (Purdue University) EE/CS 3-180
12:30p-2:00a Lunch    
2:00p-2:30p Engineering protein structure and function with theoretical protein design Jeffery G. Saven (University of Pennsylvania) EE/CS 3-180
2:35p-2:50p Modeling ensembles of transmembrane beta-barrel proteins Jérôme Waldispühl (Massachusetts Institute of Technology) EE/CS 3-180
2:55p-3:25p Coffee   EE/CS 3-176
3:25p-3:40p Exact methods for simplified protein models Rolf Backofen (Albert-Ludwigs-Universität Freiburg) EE/CS 3-180
3:40p-4:10p Discussion forum   EE/CS 3-180
4:10p-4:25p Group Photo    
4:30p-6:00p Reception and Poster Session
Lind Hall 400
Topological analysis of DNA-binding protein complexes Soojeong Kim (University of Iowa)
Overall rotation due to internal motions in the N-body dynamics of protein molecules Florence J. Lin (University of Southern California)
Simulating protein conformations by a geometric model Antonio Mucherino (Seconda Università di Napoli)
Protein folding by ZAM & FRODA Sefika Banu Ozkan (Arizona State University)
Computing conformational free energy by deactivated morphing Sanghyun Park (Argonne National Laboratory)
Minima Hopping within an all-atom framework for biomolecular structure prediction Shantanu Roy (Universität Basel)
Investigation of the unfolding pathway of Cyt2Aa2 toxin Anchanee Sangcharoen (Mahidol University )
Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding Jin Wang (SUNY)
Mathematical methods for implicit solvent models Guowei Wei (Michigan State University)
The Dynamic Nature of the Folded and Unfolded States of the Villin Headpiece Helical Subdomain: An ultrafast folding protein Lauren Wickstrom (SUNY)
A novel method for protein folding shape description Jiaan Yang (MicrotechNano)
Temperature dependence of Trp-cage folding kinetics from replica exchange simulations Sichun Yang (University of Chicago)
  Tuesday, January 15
Morning Theme: Systems modeling
Afternoon Theme: Conformational exploration, routes, and searching
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-9:30a Simulation methods for stochastic chemical systems that arise from a random time change representation David F. Anderson (University of Wisconsin) EE/CS 3-180
9:35a-10:05a Coarse-grained parameterizations of biomolecular systems Peter R. Kramer (Rensselaer Polytechnic Institute) EE/CS 3-180
10:10a-10:40a From chemical reaction systems to cellular states: A computational approach Hong Qian (University of Washington) EE/CS 3-180
10:40a-11:10a Coffee   EE/CS 3-176
11:10a-11:40a Computational experiments in coarse-graining atomistic simulations Yannis G. Kevrekidis (Princeton University) EE/CS 3-180
11:40a-1:30p Lunch    
1:30p-2:00p Using motion planning to study molecular motions Nancy M. Amato (Texas A & M University) EE/CS 3-180
2:05p-2:35p Geometrical methods for the efficient exploration of protein conformation space Evangelos A. Coutsias (University of New Mexico) EE/CS 3-180
2:40p-3:10p Network models for protein dynamics and allostery: Application to GroEL-GroES Ivet Bahar (University of Pittsburgh) EE/CS 3-180
3:10p-3:40p Coffee   EE/CS 3-176
3:40p-4:10p Structural control of motions? Robert L. Jernigan (Iowa State University) EE/CS 3-180
4:15p-4:45p The network of sequence flow between protein structures Ron Elber (University of Texas) EE/CS 3-180
4:50p-5:20p Discussion forum   EE/CS 3-180
  Wednesday, January 16
Morning Theme: Nonequilibrium & single molecules
Afternoon Theme: Nucleic acids & genomes
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-9:30a Exploring global energy landscape of lattice protein models via Monte Carlo methods Samuel Kou (Harvard University) EE/CS 3-180
9:35a-10:05a Mathematical models of folded and unfolded protein ensembles Gregory S. Chirikjian (Johns Hopkins University) EE/CS 3-180
10:10a-10:25a Current issues in understanding complex biological networks Hans G. Othmer (University of Minnesota) EE/CS 3-180
10:30a-11:15a Coffee   EE/CS 3-176
11:15a-11:45a Improving nonequilibrium free energy estimates by enhancing phase space overlap Christopher Jarzynski (University of Maryland) EE/CS 3-180
11:45a-2:00a Lunch    
2:00p-2:30p The electrostatic free energy landscape for nucleic acid folding - beyond the Poisson-Boltzmann equation Shi-Jie Chen (University of Missouri) EE/CS 3-180
2:35p-2:50p Annotated tertiary interactions in RNA structures reveal new interactions, correlations in motifs and composite motifs Christian E. Laing (New York University) EE/CS 3-180
2:50p-3:20p Coffee   EE/CS 3-176
3:20p-3:35p Mapping evolutionary pathways of HIV-1 drug resistance using conditional selection pressure Christopher J. Lee (University of California) EE/CS 3-180
3:40p-4:10p Discussion forum   EE/CS 3-180
  Thursday, January 17
Morning Theme: Protein folding & low-resolution modeling
Afternoon Theme: Protein design and interactions
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-9:30a Free energies and kinetics of protein folding from coarse master equations Gerhard Hummer (National Institutes of Health (NIH)) EE/CS 3-180
9:35a-10:05a Entropic and enthalpic barriers in cooperative protein folding Hue-Sun Chan (University of Toronto) EE/CS 3-180
10:10a-10:40a The energy landscape for folding and molecular motors José Nelson Onuchic (University of California, San Diego) EE/CS 3-180
10:40a-11:25a Coffee   EE/CS 3-176
11:25a-11:55a Transition states in protein folding Thomas Weikl (Max Planck Institute for Colloids and Interfaces) EE/CS 3-180
12:00p-12:15p Probing the diversity of unfolding pathways by simulated thermal denaturation Andrew J. Rader (Indiana University-Purdue University) EE/CS 3-180
12:30p-2:00a Lunch    
2:00p-2:30p Structure-based maximal affinity model predicts small-molecule druggability Alan C. Cheng (Amgen Cambridge Research Center) EE/CS 3-180
2:35p-2:50p Cluster optimization in protein docking Julie C. Mitchell (University of Wisconsin) EE/CS 3-180
2:50p-3:20p Coffee   EE/CS 3-176
3:20p-3:50p Multistage optimization for protein-protein docking Sandor Vajda (Boston University) EE/CS 3-180
3:55p-4:25p Discussion forum   EE/CS 3-180
6:30p-8:30p Workshop Dinner   Caspian Bistro
2418 University Ave SE
Minneapolis, MN 55414
612-623-1133 
  Friday, January 18
Theme: Big Simulations of atomically detailed models
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-9:30a The limitations of temperature replica exchange (T-REMD) for protein folding Jed W. Pitera (IBM Research Division) EE/CS 3-180
9:35a-10:05a Simulations on BlueGene of a fast folding mutant of lambda(6-85) William Swope (IBM) EE/CS 3-180
10:05a-10:50a Coffee   EE/CS 3-176
10:50a-11:20a Simulations of peptide folding and dynamics Krzysztof Kuczera (University of Kansas) EE/CS 3-180
11:25a-11:55a Discussion forum   EE/CS 3-180
11:55a-12:10p Concluding remarks Ken A. Dill (University of San Francisco), Sorin Istrail (Brown University) EE/CS 3-180

LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
Hoda Abdel-Aal Bettley Pharmacy Department University of Manchester
Nancy M. Amato Department of Computer Science Texas A & M University
David F. Anderson Department of Mathematics University of Wisconsin
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
Rolf Backofen Institute of Computer Science Albert-Ludwigs-Universität Freiburg
Ivet Bahar Department of Computational Biology University of Pittsburgh
Nathan A. Baker Department of Biochemistry and Molecular Biophysics Washington University School of Medicine
Daniel J. Bates Institute for Mathematics and its Applications University of Minnesota
John Baxter Institute for Mathematics and its Applications University of Minnesota
Yermal Sujeet Bhat Institute for Mathematics and its Applications University of Minnesota
Victor Bloomfield Department of Biochemistry University of Minnesota
Jamie Blundell Department of Physics University of Cambridge
Khalid Boushaba Department of Mathematics Iowa State University
Maria-Carme T. Calderer School of Mathematics University of Minnesota
Hannah Callender Institute for Mathematics and its Applications University of Minnesota
Hue-Sun Chan Department of Biochemistry University of Toronto
Shi-Jie Chen Department of Physics University of Missouri
Alan C. Cheng   Amgen Cambridge Research Center
Gregory S. Chirikjian Department of Mechanical Engineering Johns Hopkins University
Ludovica Cecilia Cotta-Ramusino Institute for Mathematics and its Applications University of Minnesota
Evangelos A. Coutsias Department of Mathematics and Statistics University of New Mexico
Lenore J. Cowen Department of Computer Science Tufts University
Isabel K. Darcy Department of Mathematics University of Iowa
Yuanan Diao Department of Mathematics and Statistics University of North Carolina - Charlotte
Ken A. Dill Department of Pharmaceutical Chemistry University of San Francisco
Yang Ding Department of Biology Boston College
Ron Elber Department of Chemistry and Biochemistry University of Texas
Claus Ernst Department of Mathematics Western Kentucky University
Elisenda Feliu Facultat de Matemàtiques University of Barcelona
Christodoulos A. Floudas Department of Chemical Engineering Princeton University
Anant Godbole Department of Mathematics East Tennessee State University
Laura Rocio Gonzalez-Ramirez Department of Mathematics CINVESTAV
Jason E. Gower Institute for Mathematics and its Applications University of Minnesota
Sergei Grudinin   INRIA Rhone-Alpes Research Unit
Esfandiar Haghverdi School of Informatics Indiana University
Omar Haq Computational Biology and Molecular Biopphysics Rutgers University
Milena Hering Institute for Mathematics and its Applications University of Minnesota
Peter Hinow Institute for Mathematics and its Applications University of Minnesota
Kenneth Hinson Department of Mathematics University of North Carolina - Charlotte
Xia Hua Department of Mathematics Massachusetts Institute of Technology
Gerhard Hummer Laboratory of Chemical Physics National Institutes of Health (NIH)
Sorin Istrail Department of Computer Science Brown University
Filip Jagodzinski Department of Computer Science University of Massachusetts
Richard D. James Department of Aerospace Engineering and Mechanics University of Minnesota
Christopher Jarzynski Department of Chemistry and Biochemistry University of Maryland
Robert L. Jernigan Baker Ctr for Bioinformatics and Biological Statistics Iowa State University
Tiefeng Jiang Department of Statistics University of Minnesota
Christopher Kauffman Department of Computer Science University of Minnesota
Yiannis N. Kaznessis Department of Chemical Engineering and Materials Science University of Minnesota
Yannis G. Kevrekidis Department of Chemicial Engineering Princeton University
Abdul Qayyum Masud Khaliq Department of Mathematical Sciences Middle Tennessee State University
Soojeong Kim Department of Mathematics University of Iowa
Debra Knisley Department of Mathematics East Tennessee State University
Dmitry A. Kondrashov Department of Biological Sciences University of Chicago
Samuel Kou Department of Statistics Harvard University
Dmytro Kozakov Department of Biomedical Engineering Boston University
Peter R. Kramer Department of Mathematical Sciences Rensselaer Polytechnic Institute
Krzysztof Kuczera Department of Molecular Biosciences University of Kansas
Christian E. Laing Department of Mathematics, Chemistry New York University
Fumei Lam Department of Computer Science Brown University
Juan Latorre Department of Mathematical Sciences Rensselaer Polytechnic Institute
Audrey Lee Computer Science Department University of Massachusetts
Christopher J. Lee Department of Chemistry and Biochemistry University of California
Michael Levitt Department of Cell Biology Stanford University
Ronald M. Levy Chemistry and Chemical Biology Rutgers University
Robert Michael Lewis Department of Mathematics College of William and Mary
Anton Leykin Institute for Mathematics and its Applications University of Minnesota
Timothy Lezon Department of Computational Biology University of Pittsburgh
Florence J. Lin Department of Mathematics University of Southern California
Andy Lorenz Department of Biology Boston College
Roger Lui Department of Mathematical Sciences Worcester Polytechnic Institute
Laura Lurati Institute for Mathematics and its Applications University of Minnesota
Christopher Michael Maloney Department of Computer Science Brown University
Yi Mao Department of Mathematics Michigan State University
Ezra Miller School of Mathematics University of Minnesota
Kenneth C. Millett Department of Mathematics University of California
Julie C. Mitchell Departments of Mathematics and Biochemistry University of Wisconsin
Alejandro Morales Valencia Department of Computational Sciences University of Guadalajara
Antonio Mucherino Departimento di Matematica Seconda Università di Napoli
Chitra Narayanan Department of Biochemistry Rutgers University
Junalyn Navarra-Madsen Department of Mathematics and Computer Science Texas Woman's University
Timothy Newman Department of Physics Arizona State University
Duane Q. Nykamp School of Mathematics University of Minnesota
David J. Odde Department of Biomedical Engineering University of Minnesota
Charles W. O'Donnell Electrical and Computer Engineering Department Massachusetts Institute of Technology
José Nelson Onuchic Department of Physics University of California, San Diego
Hans G. Othmer Department of Mathematics University of Minnesota
Sefika Banu Ozkan Department of Physics Arizona State University
Sanghyun Park Mathematics and Computer Science Division Argonne National Laboratory
Ioannis Paschalidis Department of Electrical and Computer Engineering,and Center for Information and Systems Engineering (CISE) Boston University
Bobby Philip Computer and Computational Sciences Division Los Alamos National Laboratory
Jed W. Pitera Almaden Research Center IBM Research Division
Andrea Pugliese Dipartimento di Matematica Università di Trento
Hong Qian Department of Applied Mathematics University of Washington
Terrance Quinn Department of Mathematical Sciences Middle Tennessee State University
Andrew J. Rader Physics Department Indiana University-Purdue University
Subramanian Ramamoorthy School of Informatics University of Edinburgh
Rahul Ravindrudu Department of Computer Science Iowa State University
Eric J. Rawdon Department of Mathematics University of St. Thomas
Stephane Redon Inovallée INRIA Rhône-Alpes
Shantanu Roy Institute of Physics Universität Basel
Anchanee Sangcharoen Institute of Molecular Biology and Genetics Mahidol University
Jeffery G. Saven Department of Chemistry University of Pennsylvania
Deena Schmidt Institute for Mathematics and its Applications University of Minnesota
Tamara Schmidt-Hegge   University of Minnesota
Brigitte Servatius Department of Mathematics Worcester Polytechnic Institute
Chehrzad Shakiban Institute of Mathematics and its Application University of Minnesota
Yang Shen Department of Biomedical Engineering Boston University
Carlos L. Simmerling Department of Chemistry SUNY
Zachariah Sinkala Department of Mathematical Sciences Middle Tennessee State University
Robert D. Skeel Department of Computer Science Purdue University
Carlos Sosa Supercomputing Institute University of Minnesota
Andrew M. Stein Institute for Mathematics and its Applications University of Minnesota
Ileana Streinu Department of Computer Science Smith College
Weitao Sun Department of Computer Science New Mexico State University
Vladimir Sverak School of Mathematics University of Minnesota
William Swope Almaden Research Center IBM
Michael Tomasini   Rutgers University
Erkan Tüzel Institute for Mathematics and its Applications University of Minnesota
George Vacek Department of Life and Materials Sciences Hewlett Packard
Sandor Vajda Department of Biomedical Engineering Boston University
Jérôme Waldispühl Applied Mathematics & CSAIL Massachusetts Institute of Technology
Jin Wang Department of Chemistry, Physics and Applied Mathematics SUNY
Zhian Wang Institute for Mathematics and its Applications University of Minnesota
Guowei Wei Department of Mathematics Michigan State University
Thomas Weikl Department of Theory and Bio-Systems Max Planck Institute for Colloids and Interfaces
Lauren Wickstrom Department of Biochemistry and Structural Biology SUNY
Sebastian Will Institute of Computer Science Albert-Ludwigs-Universität Freiburg
Di Wu Department of Mathematics Western Kentucky University
Zhijun Wu Department of Mathematics Iowa State University
Jiaan Yang   MicrotechNano
Sichun Yang Department of Biochemistry and Molecular Biology University of Chicago
Ya-xiang Yuan Institute of Computational Mathematics and Scientific/Engineering Computing Chinese Academy of Sciences
Adam Zemla Computing Applications & Research, BACE Lawrence Livermore National Laboratory
Hongchao Zhang Institute for Mathematics and its Applications University of Minnesota
Carol L. Ecale Zhou Computing Applications and Research Lawrence Livermore National Laboratory

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