Session A - Monday-Tuesday Poster Session
1. Kersey A. Black* and K. N. Houk, The Claremont Colleges and UCLA.
Cope Rearrangement of Alkenes, Allenes, and Alkynes. A Theoretical Investigation.
2. Andrzej B. Buda* and Kurt Mislow, Princeton University.
Numerical Application of the Hausdorff Set Theory to Quantification of Chirality.
3. Frank E. Blaney, Smithkline Beecham Pharmaceuticals.
Real-Time Comparison of Electrostatic Vector Fields and Their Use in Drug Design. A Theoretical Study of Interactions in G-Protein Coupled Receptor Models.
4. Tore Brink*, Jane S. Murray, and Peter Politzer, University of New Orleans.
Calculated Electrostatic Potentials and Average Local Ionization Energies: A Molecular Surface Approach.
5. Bernard K. Brooks*, Milan Hodoscek, and Peter J. Steinbach, NIH.
Comparison of Implicit and Explicit Water Models for Molecular Dynamics Simulations Exploring the Hydration and Solvation of Proteins.
6. Frank K. Brown* and Timothy N. C. Wells, Glaxo Research Institute.
A Thermodynamic Free Energy Perturbation Study of Y34 to F34 for Tyrosyl tRNA Synthetase Water Mediated Binding?
7. Louis Carlacci* and Walter Englander, University of Pennsylvania School of Medicine.
The Loop Problem in Proteins: A Monte Carlo Simulated Annealing Approach.
8. [withdrawn] B. V. Cheney and E. W. Thomas, Upjohn.
Exploration of the Potential Surfaces for the Methylation of 1-Methyl-5-ethyl-1,2,3,4-tetrazole.
9. Janet Cicariello* and Charles M. Cook, Hoffmann-LaRoche.
Modeling and Automated Design of Potential Protein Binding Peptides Using SYBYL.
10. Piotor Cieplak* and Peter A. Kollman, University of Warsaw and University of California, San Francisco.
Peptide Mimetics as Enzyme Inhibitors: Use of Free Energy Perturbation Calculations to Evaluate Ethylene Isosteres as Replacement for Amide Bonds in a Potent HIV Protease Inhibitor.
11. Shashikala G. Das* and Donald L. Dorsey, Wright Patterson Air Force Base.
Semi-Empirical, Self-Consistent Calculations of (2x2) and (sqrt19xsqrt19) Surface Reconstructions of the GaAs B Surface.
12. DeLos F. DeTar, Florida State University.
A New Method for Comparing Ab Initio Energies and for Relating them to Enthalpies of Formation.
13. Kerwin Dobbs, DuPont.
Reactions of Hydrogen and Silyl Radicals.
14. Xiping Long, Rich Graham, and Shepard Smithline*, Cray Research Institute.
A Combined Density Functional-Molecular Mechanical Study of Catalysis of Phospholipase A2 and Some Preliminary Results of a Quantum Based Molecular Dynamics.
15. Jeffrey D. Evanseck* and M. Karplus, Harvard University.
Vibrational States of Carbonmonoxyheme Proteins.
16. [withdrawn] David C. Feller and Marc S. Collett, MedImmune.
Dipeptide Backbone Conformation and Antibody Recognition of a Viral Octapeptide Epitope.
17. C. K. Foley*, L. G. Pedersen, P. S. Charifson, T. A. Darden, A. Wittinghofer, E. F. Pai, and M. W. Anderson, Cray Research and NIEHS.
Simulation of the Solution Structure of the H-ras p21-GTP Complex.
18. J. E. Bundens, L. E. Chirlian, and Michelle M. Francl*, Bryn Mawr College.
A Theoretical Characterization of the High (and Low) Points on the AL-R Insertion Pathway.
19. Jiali Gao, SUNY Buffalo.
Determination of the Aqueous Polarization Effects by Monte Carlo QM/MM Simulations.
20. Joseph T. Golab*, Martin W. Feyereisen, Rick A. Kendall, Jeff Nichols, and David Dame, Amoco Chemical, Pacific Northwest Laboratory, The Utah Supercomputing Institute, and the IBM Corporation.
An Implementation of the Direct SCF and RPA Methods on Loosely Coupled Networks.
21. Stelian Grigoras*, G. C. Lie, T. J. Barton, S. Ijadi-Maghsoodi, Y. Pang, J. Shinar, Z. V. Vardeny, K. S. Wong, and S. G. Han, Dow Corning, IBM, Iowa State University, and University of Utah.
Theoretical Simulation and Interpretation of Experimental Data - Structure Elucidation of Polydiethynylsilane for NLO Applications.
22. Peter D. J. Grootenhuis*, R. Schrijvers, and C. A. G. Haasnoot, Organon Scientific Development Group.
Development and Evaluation of the Specialized Carbohydrate Force Field CHEAT.
23. Sharon Hammes-Schiffer* and Hans C. Anderson, Stanford University.
Quantum Molecular Dynamics Using Totally Unrestricted Hartee-Fock Theory.
24. David S. Hartsough* and Kenneth M. Merz Jr., Pennsylvania State University.
Protein Solvation in Aqueous and Non-Aqueous Media.
25. Kenneth Haug, Lehigh University.
Absorption Spectra Calculations by Mixed Quantum-Classical Methods.
26. Milan Hodoscek*, Stanley Irwin, and Bernard R. Brooks, NIH.
Parallel Methods for Molecular Dynamics on MIMD Machines.
27. Yasuyuki Ishikawa* and H. M. Quiney, University of Puerto Rico and University of Oxford.
Relativistic Many-Body Perturbation-Theory Calculations Based on Dirac-Fock-Breit Wave Functions.
28. Diane Joseph-McCarthy*, Gregory A. Petsko, and Martin Karplus, MIT, Brandeis, and Harvard.
Hinged 'Lid' Motion of the Triosephosphate Isomerase Loop.
29. Gregory King* and Robert Barford, USDA, ARS, ERRC.
Calculation of Association Free Energies of Sulfonamide/Beta-Cyclodextrin Complexes.
30. Gerhard Klebe* and Thomas Mietzner, BASF-AG.
An Efficient Method to Generate Biologically Relevant Conformations of Drug Molecules.
31. Istvan Kolossvary* and Wayne C. Guida, CIBA-GEIGY Corporation.
Torsional Flexing: Conformational Searching of Cyclic Molecules in Biased Internal Coordinate Space.
32. Krzysztof Kuczera, University of Kansas.
Simulation Axial Contacts in HbS: The Other Side of Sickling.
Session B - Wednesday-Thursday Poster Session
1. Yi-Ping Liu* and Donald J. Truhlar, University of Minnesota.
New Approaches for Modeling the Dynamics of Chemical Reactions.
2. Jeffry D. Madura* and Richard H. Maughon, University of South Alabama.
Simulation of Antifreeze Peptides at the Ice/Water Interface.
3. Charles J. Manly* and Greg Durst, DowElanco Discovery Research.
The Application of Sequential Evolutionary Optimization Methodology to Refinement of Comparative Molecular Field Analysis Models.
4. Eric Martin*, Don Fontaine, Patricia Tillotson, and Greg McRae, DowElanco, Dow Chemical USA, and Carnegie Mellon University.
GRASP: Global Sensitivity Analysis in Environmental Mobility Assessment.
5. Jorge A. Medrano* and D. Dudis, AdTech Corp. and Wright Laboratories.
Semi-Empirical SCF Calculation of the Geometrical and Electronic Structures of Quasi-Particles in Polyacetylene.
6. Shuichi Miyamoto* and Peter A. Kollman, University of California, San Francisco.
Absolute and Relative Binding Free Energy Calculations of Biotin and Its Analogs to Avidin Using Molecular Dynamics/Free Energy Perturbation Approaches.
7. Henry T. Kalinoski, A. Cece, and Karl F. Moschner*, Unilever Research U.S.
Molecular Modeling of Collision-Induced Dissociation Mass Spectra of Cationized Alcohol Ethoxylate Surfactants.
8. R. Nirmala*, G. Ravishanker, and D. L. Beveridge, Wesleyan University.
Molecular Dynamics Simulation of the Canonical B d(CGCGAATTCGCG)2.
9. Klara Osapay* and David A. Case, The Scripps Research Institute.
Chemical Shift Calculations Applied for Proteins in NMR Structure Determination.
10. Arno Papazyan* and Mark Maroncelli, Pennsylvania State University.
Computer Simulations of Polar Solvation and Dielectric Friction in a Brownian Dipole Lattice.
11. Jorge M. Seminario* and Peter Politzer, University of New Orleans.
Comparison of Energies: DFT Versus Precise Ab Initio.
12. Thomas Simonson* and Axel T. Brunger, Yale University.
Thermodynamics of Protein-Peptide Interactions in the Ribonuclease-S System Studied by Molecular Dynamics and Free Energy Calculations.
13. Charles W. Ulmer II and Douglas A. Smith*, The University of Toledo.
Torquoselectivity and Hyperconjugation in the Nazarov Cyclization: The Effects of Inner Versus Outer Beta Methyl and Beta Silyl Groups.
14. James J. P. Stewart, Stewart Computational Chemistry.
Rapid Semiempirical Calculation of the Electronic Band Structures of Polymers.
15. (a) Terry R. Stouch* and Howard E. Alper, Bristols-Myers Squibb Pharmaceutical Research Institute.
Molecular Dynamics Simulations of Lipid Membranes: Water-Lipid Interactions.
(b) Terry R. Stouch* and Donald E. Williams, Bristols-Myers Squibb and University of Louisville.
Conformational Dependence of Electrostatic Potential Derived Charges of a Lipid Headgroup: Glycerylphosphorylcholine.
16. John E. Straub*, A. Rashkin and D. Thirumalai, Boston University.
A General Method for Measuring the Rate of Conformational Sampling and Energy Transfer in Proteins Using Molecular Dynamics Simulation.
17. Roberta Susnow*, Thomas Thacher, Clarence Schutt, and Herschel Rabitz, Wyeth-Ayerst Research.
Sensitivity Analysis of Beta-Turn Structures.
18. Yuji Takaoka*, Akihiro Kusumi, Hiroo Miyagawa, Marta Pasenkiewicz-Gierula, and Kunihiro Kitamura, Taisho Pharmaceutical Co., Ltd.
Molecular Dynamics Simulation of Phospholipid Bilayer in Water.
19. Alexander Tropsha*, Yibing Yan, Jan Hermans, and Bruce W. Erickson, University of North Carolina at Chapel Hill.
Relative Stability of Ace-L1-L2-Mam Dipeptides in Types 1, 1', 2 and 2' Beta-Turn Conformations from Free Energy Simulations.
20. Janice R. Ugolini*, Pallavour S. Subramanian, and Kechia J. Chou, Texaco.
Charge Calculations for Zeolite Atoms.
21. Gennady Verkhivker* and Ron Elber, University of Illinois at Chicago.
Microscopic Modeling of Ligand Diffusion Through a Protein: Carbon Monoxide in Leghemoglobin.
22. Noham Weinberg* and Saul Wolfe, Simon Fraser University.
A Novel and Highly Efficient Algorithm for the Theoretical Conformational Analysis of Cyclic Structures.
23. James Turner, Hon Chun, Steve Gallion, Paul Weiner*, John Nicholas, Chandra Singh, Moldyn, Amber Systems, Battelle Pacific Northwest Labs, and Scripps Research Clinic.
Application of Innovative Variable Reduction Techniques to Molecular Dynamics.
24. S. Vijayakumar*, Rex F. Pratt, and David L. Beveridge, Wesleyan University.
MD Studies on Beta-Lactamase from S. aureus PC1.
25. Stephen R. Wilson* and Frank Guarnieri, New York University.
Simulated Annealing of Rings.
26. C. F. Wong, Mount Sinai School of Medicine.
Sensitivity Analysis Approach to Molecular Modeling: Concepts, Tools, and Preliminary Results.
27. Robert J. Woods*, Christopher J. Edge, Raymond A. Dwek, University of Oxford.
Substituent Effects on the Conformation of N- and O-Glycosidic Linkages: A Theoretical Analysis.
28. Eve Zoebisch, SRI International.
Applications of Neural Nets to Determine Relationships Between Parameters in Force Field Development.
29. Thomas A. Halgren, Merck Research Laboratories.
The Merck Molecular Force Field: Form, Scope, Parameterization and Performance.
30. John McKelvey, Eastman Kodak.
Prediction of Geometry and Dipole Moments with Density Functional Theory as Compared to Ab Initio and Semi-Empirical Methods.
Copyright © 2007-2009. All rights reserved.
Updated March 2009.
Webmaster: Donald B. Boyd, Ph.D., Indiana University-Purdue University at Indianapolis (IUPUI)