Pre-registered Posters 2000

Gordon Research Conference on Computational Chemistry

Posters are listed alphabetically by last name, except for those presenting multiple posters.

* = Presenter on multi-author posters.

Presented Monday and Tuesday

1. Measure of stability basins for biomolecules using vector Lyapunov functions.
Ioan Andricioaei* and Martin Karplus, Harvard University.

2. Specific amino acid recognition by native and mutant Aspartyl-tRNA synthetase: Insights from Poisson-Boltzmann and molecular dynamics calculations.
Georgios Archontis*, Thomas Simonson and Martin Karplus, Dept. of Physics, University of Cyprus, Cyprus.

3. A widely applicable set of 2_D descriptors.
Wolfram Altenhofen, Chemical Computing Group Inc., Germany.

4. The AM1-BCC charge model for organic small molecules.
Araz Jakalian, David B. Jack, and Christopher Bayly*, Merck Frosst Centre for Therapeutic Research, Quebec.

5. Optimal multi-body integrator and multiple time step method for molecular dynamics.
Dmitri Beglov*, Valeri Karlov, Glenn Webb, Carlos Padilla, Moldyn, Inc.

6. Evaluation of structural models of proteins using neural networks.
Nora Benhabiles*, P. Lacknerl, F. Domingues, S. Wegenkittl, and M. Sippl, Center for Applied Molecular Engineering, University of Salzburg, Austria.

7. The use of TAE-based electron density-derived wavelet coefficient. Descriptors and semi-supervised learning in QSAR, QSPR, and ADME applications.
Curt M. Breneman*, Mark Embrechts, Kristin Bennett, Larry Lockwood, and Matthew Sundling, Departments of Chemistry, Decision Sciences and Engineering Systems, and Mathematics, Rensselaer Polytechnic Institute.

8. Folding mechanism and free energy surface of a three-stranded antiparallel beta-sheet peptide.
Philippe Ferrara and Amedeo Caflisch*, Department of Biochemistry, University of Zurich.

9. Characterizing the internal motions of peptides with MD and NMR: From crystalline amino acids to conotoxins.
David Chatfield*, Sergio Wong, and Alberto Augsten, Florida International University.

10. Extending the power of combined quantum mechanical and classical mechanical methods - Molecular properties and multi-layer partition in QM/MM methods.
Quang Cui* and Martin Karplus, Department of Chemistry and Chemical Biology, Harvard University.

11. Polarizable force field development: Improved dielectric properties of water models and implications for carbohydrate modeling.
Wolfgang Damm* and Wilfred van Gunsteren, Laboratory for Physical Chemistry, Swiss Federal Institute of Technology, ETH.

12. QM/MM study using density functional and the double link atom method.
Debananda Das*, Eric M. Billings, Bernard R. Brooks, Laboratory of Biophysical Chemistry, NIH.

13. Conceptual and computational density functional theory in the study of charge distributions and chemical reactivity: Recent developments.
F. De Proft* and P. Geerlings, Eenheid Algemene chemie (ALGC), Free University of Brussels, Brussels, Belgium.

14. Enthalpy for everyman and everywoman or the computational thermochemistry of organic compounds.
DeLos F. DeTar, Department of Chemistry, Florida State University.

15. Developments in Gaussian and other model chemistries with particular reference to compounds containing 3rd row atoms.
Brian J. Duke* and Vinutha Ramakrishna, Northern Territory University, Australia.

16. Determination of protein families by threading: Use of linear optimization.
Jaroslaw Meller and Ron Elber*, Department of Computer Science and the Cornell Theory Center, Cornell University.

17. The GRID/CPCA method: A new computational tool to design selective ligands.
Mika A. Kastenholz, Manuel Pastor, Gabriele Cruciani, Eric E. J. Haaksma, and Thomas Fox*, Department of Chemical Research/Structural Research, Boehringer Ingelheim Pharma KG, 88397 Biberach, Germany.

18. Alternate pathways for reduction of ketones by alkylaluminum reagents: Single electron transfer?
Deepa Jeyakumar, Pamela R. Seida, Michelle M. Francl*, Department of Chemistry, Bryn Mawr College.

19. A novel energy based stochastic algorithm applied to problems in protein structure prediction.
Meir Glick and Amiram Goldblum*, Department of Medicinal Chemistry, Hebrew University of Jerusalem, Israel.

20. Hybrid QM/MM simulations and non-linear spectroscopy.
I. R. Gould*, H. Amer, S. Abend, I. P. Mercer, and D. Klug, Department of Chemistry, Imperial College, London.

21. A new method for computational design of proteinomimetics: Conformationally constrained backbone cyclic peptides.
Carina Hazan* and Chaim Gilon, Institute of Chemistry, The Hebrew University of Jerusalem, Israel.

22. Catalytic inhibition of glycogen phosphorylase by a set of glucopyranose hydantoin derivatives: A free energy perturbation study.
Georgios Archontis, Dept. of Physics, University of Cyprus, Cyprus.

23. Reversible peptide folding: Dependence on the molecular force field used.
Wolfgang Damm* and Wilfred van Gunsteren, Laboratory for Physical Chemistry, Swiss Federal Institute of Technology, ETH Zurich.

24. In search for radiation-induced radicals in sugars: DFT calculation of EPR spectroscopic properties.
F. De Proft*, P. Lahorte, F. Callens, P. Geerlings, and W. Mondelaers, Eenheid Algemene chemie (ALGC), Free University of Brussels, Brussels, Belgium.

25. Accounting for environmental effects in ab initio calculations of proton transfer barriers.
M. A. Lill, M. C. Hutter, and V. Helms*, Max-Planck-Institute of Biophysics, Frankfurt.

26. Structure aided design, synthesis, and biological evaluation of combinatorial libraries for the inhibition of human rhinovirus 3C protease.
T. F. Hendrickson*, F. Chan, T. O. Johnson, S. S. Chu, P. S. Dragovich, B. W. Eastman, Y. Hua, H. T. Luu, S. H. Reich, D. J. Skalitzky, Y. Yang, S. H. Fuhrman, D. M. DeLisle. E. L. Brown, D. A. Matthews, A. K. Patick, C. E. Ford, J. W. Meador III, S. W. Worland, Agouron Pharmaceuticals, Inc.

27. QSAR: Difficult conceptual problems and some simple concrete solutions.
William C. Herndon* and Gabrielle Rum, Department of Chemistry, University of Texas at El Paso.

28. Structural changes in nucleoprotein complexes studied with flourescence resonance energy transfer (FRET).
A. Hillisch*, M. Lorenz, D. Payet, A. A. Travers, S. Diekmann, EnTec GmbH, Germany.

29. Modeling tools for high throughput drug design.
Dragos Horvath, Cerep.

30. Non-bonded interactions in flexibly optimized steric and electrostatic field alignments of drugs: Parametrisation for intramolecular pi/pi-stacking.
Hongming Chen and Axel Jensen*, Pharma Research, Medicinal Chemistry Research Institute.

31. Mechanism of inhibition of HIV-1 integrase by G-tetrad forming oligonucleotides in vitro.
Naijie Jing*, Christophe Marchand, Jie Liu, Rahul Mitra, Michael E. Hogan, and Yves Pommier, Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston.

32. The quest for a stable silyne: The role of bulky alkoxy, alkyl and aryl substituents.
Miriam Karni* and Yitzhak Apeloig, The Department of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Technion-Israel Institute of Technology, Israel.

33. Molecular electrostatic properties and polarisation effects in prediction of hydrogen bond basicity.
Peter W. Kenny, AstraZeneca, Mereside, Alderley Park, Macclefield SK10 4TG.

34. An evaluation of methods for shape and electrostatic characterization of small molecules.
Douglas B. Kitchen, Albany Molecular Research, Inc.

35. COSMOtherm: Quantum chemistry for the calculation of thermodynamic data for computational chemistry and chemical engineering.
Andreas Klamt* and Frank Eckert, COSMOlogic GmbH&CoKG, Leverkusen, Germany.

36. Hessian-free low-mode conformational search for large scale protein look optimization: Application to c-Jun N-Terminal kinase JNK3.
Istvan Kolossvary*, Laszlo Molnar, and Gyorgy M. Keseru, Novartis Institute for Biomedical Research, Novartis Pharmaceuticals.

37. A rigorous procedure for combining molecular dynamics and Monte Carlo simulation algorithms.
Laura J. LaBerge* and John C. Tully, Department of Chemistry, Yale University.

38. Structural and hydration changes in the A to B transition of DNA.
Fabrice Leclerc*, Swarnalatha Yeturu, and Martin Karplus, Universite Louis Pasteur, Strasbourg.

39. The allosteric mechanism of the molecular chaperonin GroEL.
Jianpeng Ma*, Paul B. Sigler, and Martin Karplus, Harvard University.

40. Molecular dynamics prediction of the DNA intercalation complexes with some anti-tumour agents.
Jan Mazerski, Department of Pharmaceutical Tech. and Biochemistry, Technical University of Gdansk, Poland.

41. Reactivity of zinc finger cores: Analysis of protein packing and electrostatic screening.
A. T. Maynard* and D. G. Covell, Laboratory of Experimental and Computational Biology, NCI, SAIC.

42. Analysis of the association processes in electron transfer systems.
Maria Cristina Menziani*, Francesca De Rienzo, Razif Gabdoulline, Pier Giuseppe De Benedetti, and Rebecca Wade, Universita di Modena e Reggio Emilia - Dipartimento di Chimica - Via Campi, Modena - Italy.


Presented Wednesday and Thursday

1. The electronegativity equalization method: A powerful tool for reactivity studies for large (numbers of) molecules.
W. Langenaeker, P. Lahorte, F. De Proft*, P. Geerlings, and J. P. Tollenaere, Theoretical Medicinal Chemistry, Janssen Research Foundation, Turnhoutseweg 30, B-2340 Beerse, Belgium.

2. Ab initio derived polarizable force field for peptides.
George A. Kaminski*, Harry A. Stern, B. J. Berne, Richard A. Friesner, Columbia University, Chemistry Department, and Ruhong Zhou, Schroedinger, Inc.

3. COMPLOPT - Protein ligand complex optimization.
Thomas Mietzner, Dep. ZHF/G, Bldg. A30, BASF-A, D-67056 Ludwigshafen, Germany.

4. Electrostatic interactions in a Spectroscopically Determined Polarizable Force Field (SDPFF): The N-Methylacetamide dimer.
B. Mannfors, N. G. Mirkin*, K. Palmo, and S. Krimm, Biophysics Research Division, University of Michigan.

5. PMF-scoring and its use in molecular docking experiments.
Ingo Muegge, Bayer Research Center, 400 Morgan Lane, West Haven, Connecticut.

6. Conformational analysis of cyclic glutamate analogues in aqueous solution - An evaluation of different hydration models.
Peter Aadal Nielsen*, Per-Ola Norrby, Jerzy W. Jaroszewski, and Tommy Liljefors, NeuroScience PharmaBiotec, Royal Danish School of Pharmacy, Department of Medicinal Chemistry, Copenhagen.

7. Continuum reaction field vs. particle-mesh Ewald treatments: RNA molecular dynamics simulations.
Mafalda Nina* and Thomas Simonson, Laboratorie de Biologie et Genomique Structurales (CNRS), I.G.B.M.C., 1-Rue Laurent Fries, 67 404 Strasbourg-Illkirch, France.

8. QM-guided molecular mechanics as a tool in asymmetric synthesis.
Per-Ola Norrby* and Torben Rasmussen, Department of Medicinal Chemistry, Royal Danish School of Pharmacy, Copenhagen, Denmark.

9. A design of the comprehensive fold recognition benchmark: Application to SeqFold training and validation.
Krzysztof Olszewski, Molecular Simulations Inc.

10. Molecular modeling of interactions between cholesterol and oxytocin receptor.
Ewa Politowska*, Rajmund Kazmierkiewicz, and Jerzy Ciarkowski, Faculty of Chemistry, University of Gdansk, Gdansk, Poland.

11. Optimizing ligand charges for maximum binding affinity. A solvated interaction energy approach.
Traian Sulea and Enrico O. Purisima*, National Research Council of Canada, Biotechnology Research Institute, Montreal, Canada.

12. Is the acetate anion stabilized by resonance of electrostatics? A systematic structural comparison.
Paul R. Rablen, Swarthmore College, Swarthmore, Pennsylvania, USA.

13. Molecular dynamics simulation studies on truncated NS3 protease of Hepatitis C virus.
B. Govinda Rao, Vertex Pharmaceuticals Inc.

14. Computer-assisted scanning of ligand interactions: Analysis of the fructose 1, 6-bisphosphatase-amp complex using free energy calculations.
Mark D. Erion, Paul D. van Poelje, and M. Rami Reddy*, Metabasis Therapeutics, Inc., San Diego.

15. A MD/QM study of the chorismate mutase catalyzed Claisen rearrangement reaction.
Adrian E. Roitberg, Biotechnology Division, National Institute of Standards and Technology.

16. CO(+2): Which spin states are preferred?
Ann M. Schmiedekamp, SmithKline Beecham Pharmaceuticals, on leave from Penn State University, Abington College.

17. An empirical Hydropathic Intermolecular Field Analysis (HIFA) for the prediction of ligand-receptor binding affinities.
Simon F. Semus, Department of Biological Chemistry, Wyeth Neurosciences.

18. Drug discovery with GPCR targets - Elementary my dear Watson!
Daniel Severance, Acadia Pharmaceuticals.

19. Generating accurate antibody loop conformations with rapidly converging MD simulations.
Viktor Hornak and Carlos Simmerling*, SUNY Stony Brook.

20. Decision support software and library design.
Tim Mitchell, John Holland, and Doug Smith*, Cambridge Discovery Chemistry and Oxford Molecular Group.

21. Blue Gene: Petaflop computing for large scale biomolecular simulation.
William Swope*, Robert Germain, Marc Snir, and lots of others, IBM Research.

22. Molecular modeling calculations on HIV-1 RT non-nucleoside inhibitors: Prediction of activity for novel 2-aryl-substituted benzimidazole analogs and comparison of results to HEPT and nevirapine inhibitors.
Marilyn B. Kroeger Smith*, Robert Rizzo, Julian Tirado-Rives, William Jorgensen, Christopher J. Michejda, David Farnsworth, and Richard H. Smith Jr., NCI-Frederick Cancer Research and Development Center, Maryland.

23. Properties of TFE/water mixtures.
Rajappa Chitra and Paul E. Smith*, Kansas State University.

24. Gas phase ab initio study of the proteolysis of alkyl and aryl triazenes.
Richard H. Smith Jr.*, Emily J. Snyder, Robin M. Carroll, Sarah A. Chenoweth, Teri J. Addeo, Nathan A. Smith, Christopher J. Michejda, Department of Chemisry, Western Maryland College and National Cancer Institute-FDRDC.

25. What effect does charge model have on quality of blood brain partitioning estimated with the use of the CPSA (Charge Partial Surface Area) descriptors?
Dennis Sprous* and Joseph M. Leonard, Tripos Inc.

26. How to generate better conformations with incremental construction algorithms.
Martin Stahl, Roche Bioscience, Palo Alto.

27. Modeling trimethoprim resistance in streptococcus pneumoniae: Loss of a single H-bond between dihydrofolate reductase and trimethoprim.
Peter J. Steinbach*, J. A. Donkersloot, A. Pikis, G. Vasudevan, and J. M. Keith, CIT and NIDCR, National Institutes of Health, Bethesda.

28. Polarization methods for large systems.
Steven J. Stuart* and Liegi Hu, Clemson University, Clemson, SC 29634 USA.

29. Calculated lifetimes of the first (v=1) hydrogen stretching excited state on hydrogen-covered H/Ge(110) germanium surface.
Ming-Shun Ho, Sho-Ching Hong, Hsiu-Feng Lu, and Ying-Chieh Sun*, Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan.

30. FLASHFLOOD: Efficient 3D field-based flexible molecular search and retrieval.
Mike Pitman, Hans Horn, Wolfgang Huber, Julia Rice, and William Swope*, IBM Research.

31. Molecular dynamics study of interactions of DNA and TATA-box binding protein.
Masaru Tateno*, Kazuhiko Yamasaki, Masashi Suzuki, AIST-NIBHT CREST Centre of Structural Biology, Ibaraki, Japan.

32. Monte Carlo QM/MM simulations of the dissociation of t-butyl chloride in aqueous solution.
Julian Tirado-Rives* and William L. Jorgensen, Department of Chemistry, Yale University.

33. Structure-based optimization of ATP-competitive KDR inhibitors.
Leticia M. Toledo-Sherman*, John Buchanan, Lucian DiPietro, Greg Habgood, Joseph L. Kim, Teresa Marshall, Stephanie Meyer, Kurt A. Morgenstern, Perry Novak, Joe Nunes, Vinod Patel, Paul E. Rose, David R. Stover, and Huilin Zhao, Kinetix Pharmaceuticals, Inc.

34. Are many-body effects important in protein folding?
Arjan van der Vaart* and Kenneth M. Merz Jr., Pennsylvania State University.

35. Stochastic optimization methods for biomolecular structure prediction.
T. Herges, W. Wenzel*, Department of Physics, Dortmund University; S. Gregurick, CARB, University of Maryland.

36. Ab initio molecular dynamics shows low-frequency mode manifolds mediate CO + CO+ --> CO+ + CO electron exchange.
Ralph A. Wheeler* and Sergei Skokov, Department of Chemisry and Biochemistry, University of Oklahoma.

37. Computational analysis of PKA-balanol interactions.
Chung F. Wong*, Philippe H. Hunenberger, Pearl Akamine, Narendra Narayana, Tom Diller, J. Andrew McCammon, Susan Taylor, and Nguyen-Huu Xuong, Department of Pharmacology, University of California, San Diego, La Jolla, California.

38. Simulation assisted protein structure determination using NMR residual dipolar couplings.
Xiongwu Wu*, Shaomeng Wang, and Bernard R. Brooks, GICCS, Georgetown University Medical Center, Washington DC, USA.

39. Ab initio molecular orbital study on metal-guanine complexes and reduction mechanism of O2 molecule by cytochrome c oxidase.
Yasunori Yoshioka, Department of Chemistry, Osaka University.

40. Submolecular motions in benzylic amide catenanes and rotaxanes.
Francesco Zerbetto, Dipartimento di Chimica "G. Ciamician", Universite degli Studi di Bologna, Italy.

41. Efficient virtual screening of large combinatorial libraries.
Joe Zhou*, Atsuo Kuki, Shenghua Shi, and Tom Thacher, Agouron Pharmaceuticals.

42. Molecular dynamics simulation of glycosylated human prion protein.
J. Zuegg* and J. E. Gready, Division of Biochemistry and Molecular Biology, John Curtin School of Medical Research, Australian National University, Canberra, Australia.


Additional posters added at the conference:

43. A Monte Carlo module for CHARMM.
Aaron R. Dinner* and Martin Karplus, University of Oxford.

44. Free energy of adsorption for protein-surface interaction at the primary structural level.
Robert Latour, Clemson University.

45. Molecular dynamics studies of the allosteric regulation of src-family tyrosine kinase enzymes.
Matthew Young* and John Kuriyan, Rockefeller University.

46. Stretch induced unfolding of proteins.
Emanuele Paci, University of Strasbourg, France.

47. Unfolding of hen egg lysozyme by molecular dynamics simulation at 300K: Insight into the role of the interdomain interface.
B. Gilquin, C. Guilbert, and D. Perahia*, University of Paris-Sud, France.

48. Quantum mechanical tunneling effects in liver alcohol dehydrogenase.
Jiali Gao*, Cristobal Alhambra, and Donald G. Truhlar, University of Minnesota.


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