Pre-registered Posters 1994

Gordon Research Conference on Computational Chemistry

* = Presenter on multi-author posters.

Monday PM Poster Session

M1. Comprehensive Analytical Treatment of Continuum Electrostatics.
Klaus-Michael Schaefer*, Martin Karplus.

M2. Effective Water Model for Protein Structures.
Jay Banks*, Richard Brower, Jianpeng Ma.

M3. Boundary Conditions in Simulations of Aqueous Ionic Solutions: A Reexamination.
James E. Roberts, Jurgen Schnitker*

M4. Conformational Equilibria for Sugars in the Gas Phase and in Nonpolar and Polar Solution.
Susan E. Barrows, Christopher J. Cramer*, Donald G. Truhlar.

M5. Study of Phenyl Ester Cleavage by Beta-Cyclodextrin: Semiempirical AM1 and Langevin Dipole Solvent Model.
Victor B. Luzhkov, Carol A. Venanzi*

M6. The Importance of Being Electrostatic.
Anthony Nicholls.

M7. Accurate Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanical and Continuum Dielectric Theory.
Dori Sitkoff*, B. Marten, Barry Hong, Richard Friesner.

M8. The Problem with Atomic Charges.
Christina Carey, Lisa E. Chirlian, Michelle M. Francl*, David M. Gange*

M9. Studies of Solute Diffusion in Biomembranes by Molecular Dynamics Simulations: Elucidation of Membrane Structure.
Terry R. Stouch*, Donna Bassolino-Kilmas, Howard E. Alper.

M10. Molecular Dynamics Simulations of Model Transmembrane Proteins.
Terry R. Stouch*, Donna Bassolino-Kilmas.

M11. Reaction Path Study of the B to Z Transition in a Six Base Pair DNA.
Ryszard Czerminski*, Ron Elber.

M12. MD Simulations of Protein Dynamics and Unfolding.
Julian Tirado-Rives*, William L. Jorgensen.

M13. Generalized Alteration of Structure and Parameters (GASP); a New Method for Free-Energy Perturbations in Systems Containing Flexible Degrees of Freedom.
Daniel L. Severance*, Jonathan W. Essex, William L. Jorgensen.

M14. Conformational Sampling Via Molecular Dynamics - Towards the Boltzmann Ensemble?
Thomas E. Cheatham*, Peter Kollman.

M15. Molecular Dynamics Simulations of the Binding of FK506 and its C9-desketo Analog to FK506 Binding Protein.
Michelle Lamb*, M. Orozco, E. R. Laird, J. Tirado-Rives.

M16. MD Simulation Study of the HIV-I Protease Cleavage Mechanism.
David C. Chatfield*, Bernard R. Brooks.

M17. Homology Modeling and Molecular Dynamics of a Single Chain Antibody.
Michael Mitchell.

M18. Molecular Simulation of Folding and Refolding of Secondary Structures in Aqueous Solution.
Alexander Tropsha.

M19. Study of Molecular Conformation Effects on Protein Titration Calculations.
Tony J. You*, Donald Bashford.

M20. The Effect of Hydrostatic Pressure on Protein Crystals Investigated by Molecular Simulation.
Darrin M. York, Tom A. Darden. Lee G. Pedersen*

M21. Salt Effects on Peptides: A Comparison of Molecular Dynamics Simulations.
Gail E. Marlow*, B. M. Pettitt.

M22. Wet Proteins and Vibrational States. Beyond Normal Modes.
Adrian Roitberg*, Mark Ratner, Ron Elber, Benny Gerber.

M23. Computational Screening of Random Peptide Libraries.
Qiang Zheng*, Donald J. Kyle.

M24. Brookhaven/Monte-Carlo Conformational Search: An Improved Tool for Predictiong Polypeptide Structure.
John S. Evans*, Alan M. Mathiowetz, Sunney I. Chan, William A. Goddard III.

M25. Molecular Alignment Hypothesis Refinement Through Comparative Molecular Field Analysis (CoMFA).
Charles J. Manly*, Robert W. DeSimone.

M26. Absorption Spectra Calculations Using Mixed Quantum/Semi-Classical Methods for Electonic-Vibrational Coupling.
Kenneth Haug.

M27. Development of a Parallel DF/MM Coupled Potential.
Robert F. Stanton*, Ken M. Merz Jr.

M28. Calculations of the Structure and Stability of C240 Using Divide-and-Conquer Density Functional Theory.
Darrin York*, Jian Ping Lu, Weitao Yang.

M29. SAM1 Semiempirical Parameters for Transition Metals.
Andrew J. Holder.

M30. The Absorption of Carbohydrates on Metal Surfaces.
Timothy M. Glennon*, Ailan Cheng, Kenneth M. Merz Jr.

M31. Analysis of Hydroxyl Radical Reactions Using AM1 Calculations.
B. Vernon Cheney.

M32. Cornell Theory Center (ctc) Proposed Computing Configuration (Early 1995).
Daniel Ira Sverdlik.

M33. An Affordable Chemical Information Sheet.
Frank Brown.

M34. A Method for Predicting Protein Structure.
Andrez Kolinski*, Marius Milik, Jeffrey Skolnick.

M35. Gas- and Aqueous-Phase Properties of p-Benzoquinone.
S. E. Boesch and R. A. Wheeler*

Wednesday PM Poster Session

W1. Geometries and Relative Energies of Some Reactive Intermediates: An Evaluation of the Performance of DFT Methods.
Olaf Wiest.

W2. Proton Affinities of Molecules Containing Nitrogen and Oxygen: Comparing Density Functional Results to Experiment.
Ann M. Schmiedekamp*, Igor A. Topol, Christopher J. Michejda.

W3. Estimating Parameters for Molecular Mechanics Force Fields.
Joseph M. Leonard.

W4. Spectroscopically Determined Force Fields: Alkanes.
Noemi G. Mirkin*, K. Palmo, S. Krimm.

W5. MMFF94: Extension, Completion and Validation of the Merck Molecular Force Field.
Thomas A. Halgren.

W6. A Comparison of Conformation Energies Calculated by Different Molecula Mechanics Methods.
Klaus Gundertofte, Tommy Liljefors, Per-Ola Norrby, Ingrid Pettersson*

W7. Steps Towards Modeling Reactivity in the Condensed State.
Sunder Ramachandran, Terry Lenz, Tony Rappe*

W8. (a) Avoiding Singularities in Annihilation/Creation of Atoms and Groups in Solution by Separation-Shifted Scaling.
M. Zacharias, T. P. Straatsma*
(b) Treatment of Rotational Isomeric States: The Use of Biasing Potentials.
T. P. Straatsma.

W9. Polypeptide Conformational Equilibria from Computer Simulations.
Amil G. Anderson*, Jessica Hoane, Christa Myers.

W10. Conformational Free Energies from Thermodynamic Integration.
Krzysztof Kuczera.

W11. Free Energies of Association of Cs+ to 18-Crown-6 Ether in Water. A Molecular Dynamics Study Including Counter Ions.
Liem X. Dang.

W12. Monte Carlo Docking and Free Energy Evaluation: Application to an FKBP-Tetrapeptide Substrate Complex.
Amedeo Caflisch*, Stefan Fischer, Martin Karplus.

W13. Enzyme-Inhibitor Interactions: Determining Free Energies of Binding for Sulfonamides Binding to Carbonic Anhydrase Using FDPB and PDLD.
Jeffrey D. Madura.

W14. Binding of Phosphorus-Containing Inhibitors to Thermolysin Studied by the Poisson-Boltzmann Method.
Jian Shen*, John Wendolowski.

W15. Lazarus Inhibitors of Human Leukocyte Elastase: Molecular Modeling as Aid to Inhibitor Design.
Richard P. Dunlap*, M. Bell, N. W. Boaz, J. Court, R. Desai, S. Eiff, C. A. Franke, D. J. Hlasta, A. J. Mura, C. Subramanyam.

W16. Molecular Recognition at the L-Alanine Receptor: Conformational Analysis of the Active Amino Acid Analogs.
Thomas J. Venanzi*, Bruce P. Bryant, Carol Venanzi.

W17. Support for a Proposed Mechanism of Action of Class A Beta-Lactamase Enzymes from Molecular Dynamics Simulations.
Timothy J. Mitchell.

W18. Do "Cationic" Neurotransmittors Bind to their Receptors as Amines of Protonated Amines?
Tommy Liljefors*, Per-Ola Norrby.

W19. GPCR_Builder. A Program for the Rapid Construction of 3D G-Protein Coupled Receptor (GPCR) Models.
Frank E. Blaney.

W20. The Design of New Stucture-Based Drugs for Poliovirus and Related Viruses Through the Use of Computational Methods.
Diane Joseph-McCarthy*, Martin Karplus, J. M. Hogle.

W21. Peptides to Peptidomimetics: A Systematic Approach Based on Constrained Analog Design.
Kalyanaraman Ramnarayan*, S. N. Rao, M. Fai Chan, V. B. Balaji.

W22. Robust Fit: A Novel Method for Molecular Superpositions.
David M. Gange*, Geoffrey Watson.

W23. A New Method for Molecular Matching of Flexible Molecules Using Simulated Annealing and Steric and Electrostatic Scoring.
Stephen D. Pickett*, Jon S. Mason.

W24. Molecular Dynamics Simulations of Polymer Chain Folding.
Eung-Yul Kim, Sunghwan Ko, Yoonso Choi, Yongdo Won*

W25. The Conformational Surface of Proteins and Protein-Ligand Complexes.
Andrew R. Leach.

W26. Computer Simulation of Molecular Self-Assembling Systems. Cyclodextrin Host-Guest Complexes as a Case Study.
Bernd Mayer, Gottfried Kohler*, Giancarlo Marconi.

W27. (a) Unrestrained MD Simulations in Oligosaccharide Conformational Analysis: Application to Man3GlcNAc2OH.
Robert J. Woods*, Christopher J. Edge, Bert Fraser-Reid, Raymond A. Dwek.
(b) Implication of the Conformations and Dynamics of Protein Surface Oligosaccharides in Protein Function.
Robert J. Woods*, Christopher J. Edge, Raymond A. Dwek.

W28. Ab Initio MO Studies of the Effects of Substituents in the 3-Position on the Pentadienyl Cation Electrocyclization.
Douglas A. Smith*, Charles W. Ulmer II.

W29. Tentative Molecular Mechanics Calculations Bring New Insights into the Mechanism of the Osmium-Catalyzed Asymmetric Dihydroxylation (AD).
Per-Ola Norrby*, Hartmuth Kolb, K. Barry Sharpless.

W30. Theoretical Calculation of Enthalpies of Formation of a Tetrahedral Intermediate and of Related Ethers and Alcohols.
DeLos F. DeTar.

W31. The Mechanism of the Degenerate Rearrangements of the Remarkably Reactive 9-Barbaralyl Cation (C9H9+) Investigated by Ab Initio Methods.
Peder Svensson.

W32. The Effect of Fluorine Substitution on 3,3-Sigmatropic Shifts in 1,5-Hexadienes.
Kersey A. Black*, K. N. Houk.

W33. Towards a Molecular Mechanics Force Field for Calculating Transition States.
Dawn Wiser*, Tony Rappe.

W34. A Kinetic Study of the MM3 Conformational Space Available for Cyclononane and Cyclononene.
Istvan Kolossvary.

W35. Solvation Effects on the Solution Conformation of Cyclic Peptide Mimetics Derived from NMR Data and Molecular Mechanics Calculations.
Hiroshi Nakamishi.

W36. Monte Carlo QM-CI/MM Simulation of Solvent Effects on the UV Blue Shift of Acetone.
Jiali Gao.

Financial support provided by:
Cray Research
Chiron Corporation
DuPont Merck Pharmaceuticals
Gordon Research Foundation
Lilly Research Laboratories
Merck Research Laboratories
Tripos Associates.

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