Midwest Computational Structural Biology Workshop

Sponsored by Michigan State University Quantitative Biology and Modeling Initiative

Organizers: Helen Geiger and Leslie Kuhn

Brook Lodge, Augusta, Michigan
April 30 – May 1, 2005

Program

Saturday, April 30

11:00-11:30	Registration	ConferenceHall
11:30-12:20	Lunch	Dining Hall
12:20-12:30	Workshop Introduction & Welcome	Conference Hall
	Flexability & Dynamics	Robert Cukier Session Chair
12:30-12:50	Protien Networks for Structural and Functional Protein Behavior	Robert Jernigan Iowa State University
12:50-1:10	Experimental and Computational Dynamics of Proteins in Crystals	George Phillips University of Wisconsin, Madison
1:10-1:30	Computational Analysis of the Assumptions Underlying Use of FRET as a Spectroscopic Ruler	Brent Krueger Hope College
1:30-1:50	An Automatic Method for Identifying Reaction Coordinates in Complex Systems	Ao Ma University of Chicago
1:50-2:10	Normal Mode Analysis of Domain Motions of S-Adenosylhomocysteine Hydrolase	Krzysztof Kuczera University of Kansas
2:10-2:30	Refreshment Break
	Structure Prediction & Folding	Michael Feig Session Chair
2:30-2:50	Controlling Entropy: The Key to Protein Design	Garland Marshall Washington University, St. Louis
2:50-3:10	Computational Protocols for Functional Annotations of Proteins	Jarek Meller Cincinnati Children's Hospital Research Foundation
3:10-3:30	A Framework for Globular Proteins	Jayanth Banavar Pennsylvania State University
3:30-3:50	Recognizing Protein Folds by Cluster Distance Geometry	Gordon Crippen University of Michigan
3:50-4:10	Refreshment Break
4:10-4:30	Modeling Proteins in the Unfolded State	Karl Freed University of Chicago
4:30-4:50	Silico Folding of Small Proteins	Ulrich Hansmann Michigan Technological University
4:50-5:10	Structural Bioinformatics Prediction of Transcription Factors and Target Sites	Hui Lu University of Illinois-Chicago
5:10-5:30	Interplay of Computation and Experiment in Studies of Microbial Pathogenesis: the Type II and Type III Secretion Mechanisms of Gram-negative Bacteria	William Wedemeyer Michigan State University
5:30-6:00	Break, and room check-in for those staying at Brook Lodge	W.E. Upjohn Hall
6:00-7:30	Dinner	Dining Hall
7:30-9:30	Poster Session with beer & sodas	Conference Hall

Sunday, May 1

7:00-8:00	Guests staying at Brook Lodge: room check-out (W. E. Upjohn Hall) and breakfast (Dining Hall)
7:30-8:00	Guests staying at Yarrow: continental breakfast (Brook Lodge Conference Hall)
	Solvation, Electrostatics, & Membrane Dynamics	Shelagh Ferguson-Miller Session Chair Conference Hall
8:00-8:20	A Molecular Dynamics Study of Water Chain Formation in the Proton-Conducting K Channel of Cytochrome C Oxidase	Robert Cukier Michigan State University
8:20-8:40	Continuum Modelling of Biomolecular Electrostatics and Diffusion	Nathan Baker Washington University, St. Louis
8:40-9:00	Efficient Simulation of Biomolecules with Implicit Solvent	Michael Feig Michigan State University
9:00-9:20	Properties of Polyunsaturated Lipids from MD Simulation	Scott Feller Wabash College
9:20-9:40	The Iteratively Matched Interface (IMI) Fast Poisson Solver for the Prediction of Membrane Protein Structures	Guowei Wei Michigan State University
9:40-9:50	Refreshment Break
	Protein Recognition & Drug Design	Gerald Maggiora Session Chair
9:50-10:10	Toward Developing New Scoring Functions for Structure-Based	Shaomeng Wang Drug Design University of Michigan
10:11-10:30	Computer Simulation of the Pharmacophore Profiles for omega-Opioid Receptor Selective Peptide Agonists	Paul Smith Kansas State University
10:30-10:50	A Hierarchical Model for Designing Protein Kinase Inhibitors	Chung Wong University of Missouri, St. Louis
10:50-11:10	Enrichment Enhancement in High Throughput Structure-based Virtual Screening through a Combination of FRED, ROCS, EON Scores and Naïve Bayesian Classification	Lakshmi Narasimhan Pfizer, Ann Arbor
11:10-11:20	Refreshment Break
	Protein Recognition & Drug Design	Leslie Kuhn Session Chair
11:20-11:40	Catch Me If You Can: A New View of the Dynamical Mechanism of Protein-protein Recognition University of Pittsburgh	Carlos Camacho
11:40-12:00	Protein Dynamics in the Catalysis by 6-Hydroxymethyl-7,8-dihydropterin Pyrophophokinase	Honggao Yan Michigan State University
12:00-12:20	Voxelized Protein Model for Fast Protein Docking and Function Prediction	Daisuke Kihara Purdue University
12:20-12:40	Modeling Flexibility in Molecular Recognition	Maria Zavodszky Michigan State University
12:40-1:30	Lunch and Farewell	Dining Hall