Pre-registered Posters 1998

Gordon Research Conference on Computational Chemistry

Tilton, New Hampshire

Monday Poster Session, June 29, 1998

Drug Design:

M1. A virtual screening approach applied to the search for trypanothione reductase inhibitors.
Dragos Horvath.
Topic: drug design.

M2. Structure based computer screening: Improved hit rates in flexible database queries by receptor mapping.
Thomas Fox. Hans Briem, Eric E. J. Haaksma.
Topic: drug design.

M3. An evaluation of methods for shape and electrostatic characterization of small molecules.
Douglas B. Kitchen.
Topic: drug design.

M4. Monte Carlo protein-ligand docking with GB/SA solvation.
Willem P. van Hoorn, Melissa Plount, and William L. Jorgensen.
Topic: solvation, drug design.

M5. Computational chemistry and the AIDD combinatorial chemistry - HTS program at Neurogen Pharmaceuticals.
Charles J. Manly, Deborah Jones-Hertzog, and Dan L. Rosewater.
Topic: drug design.

M6. Design, synthesis and characterization of HIV-1 PR inhibitors that are less affected by resistance mutations.
Fredy Sussman, Luis A. Martinez, Juan F. Correa, F. Javier Sardina, Jacques Ermolieff, M. Carmen Villaverde, and Jordan Tang.
Topic: drug design, free energy calculations.

M7. Binary QSAR: A new method for the determination of quantitative structure-activity relationships.
Paul Labute and C. Williams.
Topic: drug design, database queries, QSAR.

M8. Combinatorial computational ligand design.
Diane Joseph-McCarthy, James M. Hogle, and Martin Karplus.
Topic: drug design.

M9. Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method.
Richard H. Smith Jr., William L. Jorgensen, Julian Tirado-Rives, Michelle L. Lamb, Paul A. J. Janssen, Christopher J. Michejda, and Marilyn B. Kroeger Smith.
Topic: drug design, free energy calculations, Monte Carlo simulations, free energy perturbation.

M10. Molecular recognition in P2 receptors: Ligand development aided by molecular modeling and mutagenesis.
Stefano Moro, Dan-Ping Guo, Emidio Camaioni, and Kenneth A. Jacobson.
Topic: drug design, biomolecular simulation.

M11. Inhibition of cytochrome P450 catalysed insecticide metabolism: A rational approach.
Gyorgy M. Keseru and Istvan Kolossvary.
Topic: drug design.

M12. Structural and modeling analysis of the basis of viral resistence to VX-478.
B. G. Rao, M. D. Dwyer, J. A. Thomson, C. T. Baker, D. D. Deininger, M. A. Murcko, R. D. Tung, M. A. Navia, and E. E. Kim.
Topic: drug design, free energy simulations.

M13. Quantitative approach to bioreceptor-ligand interaction.
M. C. Menziani, F. Fanelli, and P. G. De Benedetti.
Topic: drug design, biomolecular simulation, quantum chemistry molecular structure/properties.

Quantum Chemisty:

M14. Assessment of recently developed GGA density functionals and comparison to the B3LYP hybrid functional.
James L. Anchell and Mark S. Stave.
Topic: quantum chemistry methods.

M15. Carbenium ions in sterol biosynthesis: Quantum mechanics and solvent effects (*).
Corky Jensen and William Jorgensen.
Topic: quantum, solvation.

M16. Asymmetry and symmetry in the molecular conformations of endosulfan.
Walter F. Schmidt.
Topic: drug design, quantum.

M17. The electronic structure of titanacycloalkenes.
Daniel Lawson and Roger DeKock.
Topic: quantum chemistry molecular structure/properties.

M18. OM2: A new semiempirical method with novel orthogonalization corrections and the electrostatic potential from its wavefunction.
Wolfgang Weber.
Topic: quantum chemistry methods, quantum chemistry molecular structure/properties.

M19. Brillouin Wigner multi-reference perturbation theory for electronic correlation effect.
W. Wenzel, M. M. Steiner, and K. G. Wilson.
Topic: quantum chemistry methods.

M20. Stabilization of the ammonium-carboxylate ion-pair by an aromatic ring.
Tommy Liljefors and Per-Ola Norrby.
Topic: quantum chemistry molecular structure/properties.

M21. Highly accurate estimates of hydrogen bond energies relying on basis set convergence patterns.
Klaus R. Liedl.
Topic: quantum chemistry methods.

M22. A challenge for density functionals: Self-interaction error increases for systems with a noninteger number of electrons.
Yingkai Zhang and Weitao Yang.
Topic: QM.


M23. Application of Ryde's QM/MM method to alcohol dehydrogenase (*).
Lars Hemmingsen, Martin Field, and Patricia Amara.
Topic: QM/MM.

M24. Combined DFT/MM potential: Geometry and vibrational frequencies of small solutes in aqueous solution.
C. Alhambra and J. Gao.
Topic: QM/MM.

M25. A QM/MM direct dynamics quasiclassical trajectory study of O-atom reaction with and alkane-thiol self-assembled monolayer.
William L. Hase and Sylvie B. M. Bosio.
Topic: QM/MM and simulation methodology.

M26. Mixed ab initio quantum mechanics/molecular mechanics methods with applications to peptides and proteins.
Dean Philipp and Richard Friesner.
Topic: QM/MM.

M27. Simulations of self-assembled monolayers on the high-tc superconductor YBa2Cu3O7.
Cyndi Wells and John T. McDevitt.
Topic: inorganic, other, QM/MM, force fields.

M28. Comparison of a variety of separation strategies of QM and MM regions in the QM/MM methods.
Milan Hodoscek and Bernie R. Brooks.
Topic: QM/MM.

Force Fields:

M29. Polycoordinated complexes of Zn2+ with models of hard (H2O, OH-) and soft (CH3SH, CH3S-) ligands.
Nohad Gresh, David Deerfield, and Lee Pedersen.
Topic: force fields.

M30. Recent developments in force field implementation.
Joseph M. Leonard.
Topic: force fields.

M31. The liquid-vapour interface of polarizable water.
V. P. Sokhan and D. J. Tildesley.
Topic: force fields/polarizability.

M32. Inclusion of atomic multipoles and polarization in force field calculations.
Carl S. Ewig, Marvin Waldman, James Kong, and Jon R. Maple.
Topic: force fields/polarizability.

M33. Force fields for ion-ligand binding: Sensitivity to electrostatic models for crown ethers and sugars in gas and condensed phases.
Randall B. Shirts, Joshua J. Harr, Darrell D. Hurt, Natalia A. Benjamin, and David M. Dastrup.
Topic: force fields, electrostatics, force fields/polarizability.

M34. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model.
Jay L. Banks, George A. Kaminski, Ruhong Zhou, Daniel T. Mainz, B. J. Berne, and Richard A. Friesner.
Topic: force fields/polarizability.

M35. Rapid parameter determination for ground and transition states from mixed quantum chemical and experimental data.
Per-Ola Norrby and Tommy Liljefors.
Topic: force fields.


M36. Computer simulations of dielectric friction and polar solvation dynamics.
P. Vijaya Kumar and Mark Maroncelli.
Topic: electrostatics.

M37. Electrostatic coupling to pH-titrating sites as a source of cooperativity in protein-ligand binding.
Velin Spassov and Donald Bashford.
Topic: electrostatics, other (cooperativity, pH titration).

M38. Dielectric screening in proteins: Implicit solvent model based on micro-environment modulated screened coulomb potentials.
E. L. Mehler, S. A. Hassan, and F. Guarnieri.
Topic: electrostatics.

M39. Continuum electrostatic energies of macromoleculrs in aqueous solutions.
Marco Scarsi, Joannis Apostolakis, and Amedeo Caflisch.
Topic: electrostatics solvation.

M40. Ensemble-averaged atomic partial charges for carbohydrate simulations.
Robert J. Woods, Ryan Chappelle, Ahammadunny Pathiaseril, Dilek Calgan, and Tereza Varnali.
Topic: electrostatics, biomolecular simulation, force fields.

Simulation Methodology:

M41. Simulations of chemical processes in solutions and proteins: The importance of proper boundary conditions.
Y. Y. Sham, J. Bentzien, and A. Warshel.
Topic: simulational methodology.

Wednesday Poster Session, July 1, 1998

Protein Folding:

W1. Folding proteins with distance geometry and predicted inter-residue distances.
Enoch Huang and Jay Ponder.
Topic: protein folding.

W2. Reversible protein folding through self-guided MD simulations.
Shaomeng Wang and Xiong-Wu Wu.
Topic: protein folding, biomolecular simulation, simulation methodology.

W3. Ab initio protein structure prediction and a comparative genetic algorithm.
Susan K. Gregurick, Jan Pedersen, and John Moult.
Topic: protein folding, conformational search.

W4. Pathways to a folding intermediate observed in a one microsecond simulation in aqueous solution.
Yong Duan and Peter A. Kollman.
Topic: protein folding.

W5. Homology model for oncostatin M based on NMR structural data.
Douglas B. Kitchen, Ross C. Hoffman, Franklin J. Moy, and Robert Powers.
Topic: protein folding, biomolecular simulation.

Free Energy:

W6. Free energy surfaces of solvated peptides.
Krzysztof Kuczera and Janaki Ananth.
Topic: free energy calculations, solvation, simulation methodology, biomolecular simulation.

W7. Analysis of the free energy of protein-DNA binding: The EcoRI endonuclease-DNA complex.
Kevin J. McConnell, B. Jayaram, Surjit B. Dixit, and D. L. Beveridge.
Topic: free energy calculations, electrostatics.

W8. Lambda-dynamics free energy calculations of binding of small molecules to an artificial protein cavity.
Zhuyan Guo and Charles L. Brooks III.
Topic: free energy calculations.

W9. Free energy simulation of protein - carbohydrate interactions.
Ahammadunny Pathiaseril and Robert J. Woods.
Topic: free energy calculations.

W10. Binding affinities of ion pairs and hydrogen-bonded base-pairs with mining minima and generalized Born model.
R. Luo, M. S. Head, J. A. Given, and M. K. Gilson.
Topic: free energy calculations.

Simulation Methodology:

W11. Continuum corrections to the polarization and thermodynamic properties of Ewald sum simulations for ions and ion pairs at infinite dilution.
Shinichi Sakane and Robert H. Wood.
Topic: simulation methods.

W12. Ionic charging free energies: Spherical vs periodic boundary conditions.
Tom Darden, David Pearlman, and Lee Pedersen.
Topic: electrostatics, free energy calculations.

W13. A comparison of ligand unbinding from native and mutant HIV-1 proteases using applied force simulations, atomistic molecular dynamics, and MBO(N)D methods.
Kenneth Butenhof, Donovan N. Chin, and David Haney.
Topic: simulation methods.

W14. Automatic body definition for multibody dynamics: Graph-theoretical clique cover approach.
Ryszard Czerminski.
Topic: simulation methodology.

W15. Fast adaptive multipole algorithm for electrostatics and Lennard-Jones (*).
Marcia Fenley, Alexander Boschitsch, and Wilma Olson.
Topic: simulation methods.

W16. Anisotropic constant pressure simulations of biomembranes using LAMMPS.
John E. Carpenter and Terry Stouch.
Topic: simulation methodology or biomolecular simulation.

W17. A gradient assisted genetic algorithm for global optimization of peptides.
Adrian E. Roitberg, Susan Gregurick, and Carlos Simmerling.
Topic: conformational search, simulation methodology.

W18. CHASM-E (CHain Alignment on the Surface of Materials - Energy method). A theoretical tool for determining the three-dimensional localization of polypeptides at surfaces. General search method and its application to polypeptide-ice and polypeptide-mineral interactions.
John Spencer Evans, Yaohua Dai, and David A. Evans.
Topic: simulation methodology/biomolecular simulations.

W19. Long time step MD simulations using split integration symplectic method.
Dusanka Janezic, Franci Merzel, and Matej Praprotnik.
Topic: simulation methodology.

W20. Symplectic methods for constant temperature molecular dynamics.
Stephen Bond, Brian Laird, and Benedict Leimkuhler.
Topic: simulation methodology, biomolecular simulation, MD algorithms.

W21. Reaction path calculation using the targeted molecular dynamics: The alanine dipeptide and the HIV-proteinase as test cases.
Philippe Ferrara, Joannis Apostolakis, and Amedeo Caflisch.
Topic: conformational search, biomolecular simulations.


W22. Molecular dynamics study of orientational relaxation near isotropic-nematic transition.
S. Ravichandran, A. Perera, M. Morea, and B. Bagchi.
Topic: other.

W23. Molecular dynamics of Staphylococcal nuclease: Comparison of simulation with 15N and 13C NMR relaxation data.
David Chatfield, Attila Szabo, and Bernard Brooks.
Topic: biomolecular simulation.

W24. Comparative studies of amphotericin B-cholesterol/ergosterol membrane channels - Molecular dynamics simulations.
Maciej Baginski, Haluk Resat, and Edward Borowski.
Topic: biomolecular simulation, drug design.

W25. Molecular dynamics simulations of ice-1h/water interfaces.
A. D. J. Haymet and Jennifer A. Hayward.
Topic: other.

W26. B-DNA's B(I)-B(II) conformer substate dynamics is coupled with water migration.
Rudolf H. Winger, Klaus R. Liedl, and Erwin Mayer.
Topic: biomolecular simulation.

W27. Computational studies of HIV protease: Reaction paths, conformational transitions, and drug resistance.
Steven W. Rick.
Topic: free energy calculations, biomolecular simulation.

W28. Amino acid protonation states determine QB and QB-binding sites in the photosynthetic reaction center from Rhodobacter sphaeroides.
Ralph A. Wheeler and Anthony Kurt Grafton.
Topic: biomolecular simulation.

W29. Modeling electron transfer from Qa to Qb in reaction center protein.
E. Alexov and M. Gunner.
Topic: biomolecular simulations.

W30. A molecular dynamics study of sequence dependent DNA bending and its sensitivity to ionic conditions.
M. A. Young, D. Sprous, and D. L. Beveridge.
Topic: biomolecular simulation, solvation.

W31. Modeling of zymogenic human coagulation factor IX.
Lalith Perera and Lee Pedersen.
Topic: biomolecular simulation.

W32. Helix-lipid interactions in glycophorin dimerization: Molecular dynamics calculations.
Tom Woolf, Alan Grossfield, Kevin MacKenzie, and Don Engelman.
Topic: biomolecular simulation, solvation, protein folding.

W33. Aromatics at interfaces: Molecular dynamics calculations of indoles in popc bilayers.
Tom Woolf and Alan Grossfield.
Topic: biomolecular simulation, solvation, protein folding.


W34. ES/IS combining models with implicit and explicit solvation to estimate conformational free energies.
Jan Hermans.
Topic: solvation, conformational search.

W35. Free energies of solvation with quantum mechanical interation energies from classical mechanical simulations.
Shinichi Sakane, Jose A. Barriocanal, Eric Yezdimer, Robert H. Wood, and Douglas Doren.
Topic: solvation.

W36. A comparison of the TIP3P, SPC and SPC/E water models. A molecular dynamics study of tryptophan in water.
O. P. Mark and L. Nilsson.
Topic: solvation, biomolecular simulation, simulation methodology.

W37. Solubility of non-polar solutes in water: Computer simulations using CF1 central force model.
A. D. J. Haymet and Jonathan W. Arthur.
Topic: solvation, free energy calculations.

W38. Effects of cosolvents on hydrophobic hydration.
Paul E. Smith.
Topic: solvation.

Conformational Search:

W39. Understanding hydrophobic hydration. Enthalpy-entropy and cavity decomposition of alkane hydration free energies.
Emilio Gallicchio, Masahito Kubo, and Ronald M. Levy.
Topic: solvation, free energy calculations.

W40. Theoretical ab initio calculation of entropy of organic compounds including compounds that exist as mixtures of conformers.
DeLos F. DeTar.
Topic: other.

W41. Reproducing the experimental tautomer distribution of 1-ethyl, 3-methyl triazene to 1-methyl, 3-ethyl triazene as a test of solvation model.
Ann M. Schmiedekamp, Anita Aucutt, Boris Sverzhin, and Brendan Myers.
Topic: solvation, quantum chemistry molecular structure/properties.

W42. Conformational sampling in biomolecular simulations: Want more? Use LES.
Carlos Simmerling, Jennifer Miller, Matthew Lee, and Peter Kollman.
Topic: conformational search, protein folding.

W43. PSS -- Smoothing algorithms for conformational search.
Rohit Pappu, Reece Hart, and Jay Ponder.
Topic: conformational search.

W44. Molecular modeling study of the ARG-GLY-ASP-SER (RGDS) cell binding domain of fibronectin.
Debananda Das and Scott L. Whittenburg.
Topic: conformational search.

Drug Design:

W45. Computational models for probing the subtype-selective dissociation behavior of a carbostyril DF-agonist with antagonist-insensitive binding.
Bigel G. J. Richards and Stephen T. Nowicki.
Topic: drug design (receptor mapping, ligand design).

Poster Schedule Addendum

Change in Scheduling:

W29. Modeling electron transfer from Qa to Qb..., Alexov and Gunner,
Switched to: M43.

Additional Poster for Monday, June 29, 1998:

M42. QM(ai)/MM free energy surfaces for enzymatic reactions: The nucleophilic attack step in subtilisin.
J. Bentzien, R. P. Miller, J. Florian, T. M. Glennon, and A. Warshel.

Additional Posters for Wednesday, July 1, 1998:

W29. The role of his64, arg45, and large-scale motions in the spectroscopic A-states of carbonmonoxy myoglobin by vaccum and liquid simulations.
Jeffrey Evanseck.
Topic: simulations.

W46. Stability of 3'-hydroxy-hexitol nucleotide/RNA complexes studied by molecular dynamics simulation.
Berthold Wroblowski and Piet Herdewijn.

W47. Guests, ligands, and side chains: Calculating relative free energies with chemical-Monte Carlo/molecular dynamics.
Jed Pitera and Peter Kollman.

W48. Amphotericin-B channels: Cation passageways and thermodynamics.
Haluk Resat and Maciej Baginski.

W49. Electrostatic cutoff corrections in free energy simulations.
Haluk Resat and J. Andrew McCammon.

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