1. Calculation of Absolute Binding Free Energies: A Quantitative Approach.
University of Vienna, Austria
2. Probing the Mechanism of Base Flipping via Potential of Mean Force Calculation.
Niu Huang*(1), Nilesh K. Banavali(2), and Alexander D. MacKerell, Jr.(1)
(1)Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland
(2)Department of Biochemistry and Structural Biology, Weill Medical College of Cornell University, NY
3. Crystallographic and Computational Studies of a Class II MHC Complex with a Nonconforming Peptide: The Preliminary Structure of HLA-DRA/DRB3*0101.
Christian S. Parry* and Lawrence J. Stern
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA
4. A structurally conserved water molecule in Rossmann fold dinucleotide-binding domains.
University of Missouri-Columbia
5. Multiconfigurational Nuclear-Electronic Orbital (NEO) Approach: Incorporation of Nuclear Quantum Effects in Electronic Structure Calculation.
Tzvetelin Iordanov*, Simon Webb, and Sharon Hammes-Schiffer
The Pennsylvania State University
6. Estimation of Binding Affinities of Celecoxib Analogs with COX-2: The VALIDATE Approach.
Gennadiy I. Poda*, Richard D. Head, and Joseph J. McDonald
Pharmacia Discovery Research, Missouri
7. Trends in the Job Market for Computational Chemists.
Donald B. Boyd
8. Symplectic Molecular Dynamics Integration.
National Institute of Chemistry, Slovenia
9. Accurate Simulation of Ion Solvation Using the TINKER Force Field.
Pengyu Ren, Alan Grossfield, and Jay W. Ponder*
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Missouri
10. QSPR Model Generation and Validation for Virtual High-Throughput Screening.
Curt M. Breneman*(1), Minghu Song(1), Nagamani Sukumar(1), Kristin P. Bennett(2), Steven Cramer(3), and Jinbo Bi(2)
Departments of (1)Chemistry, (2)Chemical Engineering, (3)Mathematics, Rensselaer Polytechnic Institute, Troy, NY
11. New developments in The TAE RECON PEST Method and Its Application to Large Database Mining, QSAR and Virtual High Throughput Screening.
Curt M. Breneman*, N. Sukumar, Quong Luo, Bo Jiang, Lingling Shen, Matt Sundling and Christopher E. Whitehead
Department of Chemistry, Rensselaer Polytechnic Institute, NY
12. Transferable Atom Equivalent Multi-centered Multipole Expansion Method.
Christopher Whitehead*(1), N. Sukumar(2), and C. M. Breneman(2)
(1)Pfizer Global Research & Development, Ann Arbor, Michigan
(2)Department of Chemistry, Rensselaer Polytechnic Institute, NY
13. Ab initio study of abnormal Michael addition.
Florida International University
14. High-Throughput Ligand Docking for Lead Discovery.
15. A Quantum Mechanics Based Study of Protein-Ligand Interaction.
Kaushik Raha* and Kenneth M. Merz, Jr.
Department of Chemistry, The Pennsylvania State University, University Park, PA
16. Locating the experimental structure of a nonhelical nucleic acid by combined locally enhanced sampling and continuum electrostatics approach.
Xiaolin Cheng* and Carlos Simmerling
Department of Chemistry, State University of New York at Stony Brook, NY
17. Prediction of hydrogen bond donor strength using computed molecular electrostatic properties.
Peter W. Kenny
18. Database mining for compounds to inhibit HIV-gp41 mediated viral-host cell membrane fusion: Docking protocol and method validation studies.
Robert C. Rizzo*, Miriam Gochin, and Irwin D. Kuntz
Department of Pharmaceutical Chemistry, University of California, San Francisco. CA
19. Development of GOLD for Virtual Screening.
Jason Cole*(1), Willem Nissink(1), Robin Taylor(1), Richard Taylor(2), Marcel Verdonk(2), Chris Murray(2), and Mike Hartshorn(2)
(1)Cambridge Crystallographic Data Centre, Cambridge, UK
(2)Astex Technology Ltd., Cambridge, UK
20. Binding mode analysis of selective insect P450 Inhibitors.
Gyoergy M. Keseru (1,2), Zoltan Kovari(2), Istvan Kolossvary*(1,3), and Jianling Wang(3)
(1)Department of Chemical Information Technology, Technical University of Budapest, Hungary
(2)Computer Assisted Drug Discovery, Gedeon Richter Ltd., Budapest, Hungary
(3)Novartis Institute for Biomedical Research, NJ
21. Effects of the introduction of alternated amide backbone modifications: Molecular dynamics simulations of 15mer DNA/RNA duplexes and single strands.
Syngenta Crop Protection AG, Basel, Switzerland
22. The Convergence Studies of Replica Exchange Method and Its Implementation in AMBER.
Guanglei Cui* and Carlos Simmerling
Department of Chemistry, SUNY at Stony Brook, NY
23. Algorithms for Computational Solvent Mapping of Proteins.
Tamas Kortvelyesi*(1,2), Sheldon Dennis(1), Michael Silberstein(3), Lawrence Brown III(1), Karl H. Clodfelter(3), and Sandor Vajda(1)
(1)Department of Biomedical Engineering, Boston University
(2)Department of Physical Chemistry, University of Szeged, Hungary
(3)Program in Bioinformatics, Boston University
24. The Reaction Mechanism of Soluble Epoxide Hydrolase: Insights from Molecular Dynamics Simulations.
Aarhus University, Denmark
25. SAR by NMR and by Computer: A Comparative Study.
F. Sirockin, C. Sich, S. Improta, M. Schaefer, V. Saudek, N. Froloff, M. Karplus, and Annick Dejaegere*
Ecole Superieure de Biotechnologie de Strasbourg, France
26. Comparative Modeling of Mycobacterium avium Complex Dihydrofolate Reductase.
Prashant S. Kharkar and Vithal M. Kulkarni*
Pharmaceutical Division, Institute of Chemical Technology, University of Mumbai, India
27. Co+2 Spin State: The effect of biologic ligands H2O, NH3 and imidazole and continuum solvation.
Ann M. Schmiedekamp*(1), and M. Dominic Ryan(2)
(1)Penn State University, Abington College, PA
(2)Millennium Pharmaceuticals, Cambridge, MA
28. Biocomputing in Drug Design: Bridging the Disciplinary Gap with Web-Based Interactive Multimedia Courseware.
Christopher Andrews, Mathieu Castonguay, Alain Deschenes, David Norman, Rodney Cooper, and Ghislain Deslongchamps*
Departments of Chemistry, Computer Science, University of New Brunswick, N.B., Canada
29. The Free Energy State of Water Hydration Layers and Its Importance for Ligand-Receptor Binding.
Garrett W. Grahek(1), Steven J. Stuart(2), and Robert A. Latour Jr.*(1)
(1)Department of Bioengineering, (2)Department of Chemistry, Clemson University, SC
30. A Kirkwood-Buff Derived Force Field for Urea/Water Mixtures.
Samantha Weerasinghe and Paul E. Smith*
Department of Biochemistry, Kansas State University, KS
31. Energetic and Conformational Aspects of Base-Pair Opening Within the DNA Double Helix.
Laboratoire de Biochimie Theorique, CNRS, France
32. The ene reactions of nitroso compounds: Theory predicts the intermediacy of a polarized diradical.
Andrew G. Leach* and K. N. Houk
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA
33. Predictions of Zinc Finger Protein Structure by Molecular Dynamics Simulations.
Roland H. Stote*(1), Esther Kellenberger(2), Herve Muller(1), Bruno Kieffer(3) and Yves Mely(4)
(1)Laboratoire de Chimie Biophysique, Strasbourg
(2)Faculte de Pharmacie, Illkirch
(3)Laboratorie de Genomique Structurale, Illkirch
(4)Pharmacologie et Physico-chimie des Interactions Cellulaires et Moleculaires, CNRS, Illkirch, France
34. Tuning an Implicit Solvent Force Field for Protein Simulations.
The Scripps Research Institute, La Jolla, CA
35. Use of Poisson-Boltzmann Molecular Dynamics in Protein Folding Studies.
University of California Irvine
36. The Conformation and Dynamics of the Complexes of Substrates and the Aromatic Amino Acid Hydroxylases.
Knut Teigen*(1), K. K. Dao(1), N. A. Froystein(2), and A. Martinez(1)
Departments of (1)Biochemistry and Molecular Biology and (2)Chemistry, University of Bergen, Norway
37. Insights into protein-protein binding by binding free energy calculation and free energy decomposition.
Holger Gohlke* and David A. Case
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA
38. Amide Mode Phi/Psi Dependence in Peptides from Theoretical Vibrational Frequency Maps.
Noemi G. Mirkin* and Samuel Krimm
Biophysics Research Division, University of Michigan, Ann Arbor, MI
39. New three-dimensional models in the design of new M4 selective agonists.
UCB Research, Inc., Cambridge, MA
40. Consensus Design: Integrating Ligand and Structure-Based Approaches.
Paulette A. Greenidge
De Novo Pharmaceuticals, Cambridge, UK
41. All Atom Structure Prediction and Folding Simulations of a Stable Protein.
Carlos L. Simmerling(1), Bentley Strockbine(1), and Adrian E. Roitberg*(2)
(1)Center for Structural Biology and Department of Chemistry, University of Stony Brook, NY
(2)Quantum Theory Project and Department of Chemistry, University of Florida
42. Comparative Molecular Field Analysis of Methylphenidate Analogues -- Drugs Potentially Useful in the Treatment of Cocaine Abuse.
Kathleen Gilbert(1), Ronald A. Buono(1), Milind Misra(1), Carol A. Venanzi*(1), Margaret M. Schweri(2), Qing Shi(3), and Howard M. Deutsch(3)
(1) Department of Chemistry and Environmental Science, New Jersey Institute of Technology, NJ
(2)Mercer University School of Medicine, Macon, GA
(3)School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
43. Studies of Activation and Inhibition Mechanisms of Calcium Channel Through QSARs of Ligands Binding to Calcium Channel.
S. P. Gupta
Birla Institute of Technology and Science, Pilani, India
44. Validating Predictions of Protein-Ligand Interaction.
J. Willem M. Nissink*(1), Chris Murray(2), Mike Hartshorne(2), Marcel L. Verdun(2), Jason C. Cole(1), and Robin Taylor(1)
(1)Cambridge Crystallographic Data Center, Cambridge, UK
(2)Astex Technology Ltd., Cambridge, UK
45. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation.
Ting Wang* and Rebecca C. Wade
European Media Laboratory and European Molecular Biology Laboratory, Heidelberg, Germany
European Molecular Biology Laboratory, Heidelberg, Germany
46. How to model the unfolded peptide backbone in solution: Comparison of simulations with MM and QM/MM.
Jan Hermans* and Hao Hu
University of North Carolina
47. Using PC Clusters to Evaluate the Transferability of Molecular Mechanics Force Fields for Proteins.
Asim Okur*, Bentley Strockbine, Viktor Homak, and Carlos Simmerling
Department of Chemistry, State University of New York, Stony Brook, NY
48. Extension of the replica/path method for more accurate modeling of complex chemical and biochemical reactions.
H. Lee Woodcock III*(1) and Bernard R. Brooks(2)
(1)Department of Chemistry, University of Georgia, GA
(2)Laboratory of Biophysical Chemistry, NHLBI, NIH, MD
49. Irreversible Inhibition of HIV-1 Protease by QM/MM -- REPLICA/PATH Method.
National Institute of Chemistry, Slovenia
50. Intrinsic Dimensionality of the Solubility Phenomenon as Derived from Mutual Solubilities of a Large Body of Chemicals Using Advanced QSAR and Chemometric Techniques.
Department of Chemistry, University of Florida, Gainsville, FL
51. Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation.
Xiongwu Wu* and Bernard R. Brooks
Laboratory of Biophysical Chemistry, NHLBI, NIH, Bethesda, MD
52. Development of soft-core potential functions for improved sampling.
Viktor Hornak* and Carlos Simmerling
Center for Structural Biology and Department of Chemistry, SUNY at Stony Brook
53. FAUST -- An Algorithm for Functional Templates Extraction from Protein Structures.
Mariusz Milik, Sandor Szalma, and Krzysztof A. Olszewski*
Accelrys, San Diego, CA
54. The relationship between protein stability and flexibility: Molecular dynamics simulations of cytochromes c.
Linghao Zhong* and Kara L. Bren
Department of Chemistry, University of Rochester, NY
55. Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins.
Michael R. Shirts*(1), Jed W. Pitera(2), William C. Swope(2), and Vijay S. Pande(1)
(2)IBM Almaden Research Center, San Jose, CA
56. Water Properties and Amino Acid Solvation: Ewald vs. Finite-Ranged Potentials.
Jed W. Pitera and William Swope*
IBM Almaden Research Center, San Jose, CA
57. Free Energy Landscape of a Beta-hairpin folding in Water: Explicit solvent vs. Implicit Solvent.
Ruhong Zhou*(1), Bruce Berne(1), Robert Germain(1), Jed Pitera(2), and William Swope(2)
(1)IBM T. J. Watson Research Center, Yorktown Heights, NY
(2)IBM Almaden Research Center, San Jose, CA
59. Ab Initio Study of Oxygen Atom Transfer from Hydrogen Peroxide to Trimethylamine.
Gianluca Ottolina* and Giacomo Carrea
Instituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
60. Covalently Attached Monolayers on Silicon Surfaces.
Louis de Smet, Ernst J. R. Sudhoelter, and Han Zuilhof*
Laboratory of Organic Chemistry, Wageningen University, Netherlands
61. Accurate Molecular Mechanics Modeling of Amide NH Out-of-Plane Deformation: Electrostatic and Valence Aspects.
Kim Palmo*, B. Mannfors, N. G. Mirkin, and S. Krimm
Biophysics Research Division and Department of Physics, University of Michigan
62. Peptide Loop-Closure Kinetics from Microsecond Molecular Dynamics Simulations in Explicit Solvent.
In-Chul Yeh and Gerhard Hummer*
Laboratory of Chemical Physics, NIDDKD, National Institutes of Health, MD
In addition to the posters above, 4-8 unrecorded posters were accepted by the vice-chairman and presented during the week.
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Updated March 2009.
Webmaster: Donald B. Boyd, Ph.D., Indiana University-Purdue University at Indianapolis (IUPUI)