Computational Chemistry
Gordon Research Conference
October 8-13, 2006

Les Diablerets Conference Center
Les Diablerets, Switzerland

Chair: Wilfred F. van Gunsteren, ETH Zurich, Switzerland
Vice Chair: Jed W. Pitera, IBM, USA

Contributors:
Novartis
Sika
Genentech
Clariant
IBM
Nestle
Boehringer Ingelheim
Journal of Computer-Aided Molecular Design published by Springer
Gordon Research Conferences

SUNDAY, 8 October 2006

4:00 pm - 7:30 pm Arrival and check-in (Welcome Apero from 5.00 pm)

6:00 pm - 7:30 pm Dinner

7:30 pm - 7:40 pm Welcome / Introductory comments (from the GRC site staff and W.F. van Gunsteren)

7:40 pm - 9:30 pm Force Fields, Polarization

7:40 pm - 7:45 pm Discussion leader: Prof. Wilfred F. van Gunsteren (ETH Zurich, Zurich, Switzerland)

7:45 pm - 8:15 pm Prof. Alexander D. MacKerell (University of Maryland, Baltimore, USA)
"Polarizable empirical force field based on the classical Drude oscillator model"

8:15 pm - 8:25 pm Discussion

8:25 pm - 8:55 pm Prof. Jay W. Ponder (Washington University Medical School, St. Louis, USA)
"Polarizable force fields: Perspective and personal experience"

8:55 pm - 9:05 pm Discussion

9:05 pm - 9:25 pm Prof. Robert Woods (University of Georgia, Athens, USA)
"Approaches to deriving internally-consistent atomic polarizabilities for use in classical simulations"

9:25 pm - 9:30 pm Discussion

9:30 pm - ... Reception

MONDAY, 9 October 2006

7:30 am - 8:30 am Breakfast

9:00 am - 12:30 pm Quantum Methods, Session in remembrance of Michael Zerner

9:00 am - 9:15 am Discussion leader: Prof. Walter Thiel (Max-Planck-Institute, Mulheim, Germany)

9:15 am - 9:45 am Prof. Richard A. Friesner (University of Columbia, New York, USA)
"A new approach to density functional thermochemistry: Empirical localized orbital corrections"

9:45 am - 10:00 am Discussion

10:00 am Photo time

10:15 am - 10:30 am Coffee break

10:30 am - 11:00 am Prof. Jurg Hutter (University of Zurich, Zurich, Switzerland)
"Large scale density functional calculations with the Gaussian and augmented-plane wave method"

11:00 am - 11:15 am Discussion

11:15 am - 11:45 pm Dr. Dirk Bakowies (ETH Zurich, Zurich, Switzerland)
"Ab initio thermochemistry without empirical corrections"

11:45 am - 12:00 am Discussion

12:00 pm - 12:20 pm Dr. Reinhold F. Fink (University of Wurzburg, Wurzburg, Germany)
"Retaining the excitation degree perturbation theory: A well defined multi-reference configuration electron structure method"

12:20 pm - 12:30 pm Discussion

12:30 pm Lunch

4:00 pm - 6:00 pm Poster Session

6:00 pm - 7:30 pm Dinner

7:30 pm - 9:30 pm Reactions

7:30 pm - 7:45 pm Discussion leader: Dr. Adrian Mulholland (University of Bristol, Bristol, UK)

7:45 pm - 8:15 pm Prof. Arieh Warshel (University of Southern California, Los Angeles, USA)
"Recent advances in simulation of biological functions"

8:15 pm - 8:25 pm Discussion

8:25 pm - 8:55 pm Prof. Bernhard H. Schlegel (Wayne State University, Detroit, USA)
"Exploring potential energy surfaces for biochemical reactions"

8:55 pm - 9:05 pm Discussion

9:05 pm - 9:25 pm Dr. Hans Martin Senn (Max-Planck-Institute, Mulheim, Germany)
"Enzymatic halogenation in the fluorinase: Insights from QM and QM/MM calculations"

9:25 pm - 9:30 pm Discussion

9:30 pm - ... Bar, Poster Session

TUESDAY, 10 October 2006

7:30 am - 8:30 am Breakfast

9:00 am - 12:30 pm Biomolecular Modeling, Session in remembrance of Peter Kollman

9:00 am - 9:15 am Discussion leader: Prof. Alan E. Mark (University of Queensland, Brisbane, Australia)

9:15 am - 9:45 am Prof. Ken A. Dill (University of California, San Francisco, USA)
"Speeding up conformational searching in all-atom folding models"

9:45 am - 10:00 am Discussion

10:00 am - 10:30 am Coffee break

10:30 am - 11:00 am Prof. Liu Haiyan (University of Science and Technology, Hefei, China)
"Using free energy surfaces to guide the improvement of models for biomolecular simulations"

11:00 am - 11:15 am Discussion

11:15 am - 11:45 pm Dr. Bernard R. Brooks (National Institutes of Health, Bethesda, USA)
"Multi-scale methods for examining macromolecular systems"

11:45 am - 12:00 am Discussion

12:00 pm - 12:20 pm Dr. Hans-Jorg Limbach (Nestle Research Center, Lausanne, Switzerland)
"Simulations of malto-oligomer water mixtures"

12:20 pm - 12:30 pm Discussion

12:30 pm Lunch

4:00 pm - 6:00 pm Poster Session

6:00 pm - 7:30 pm Dinner

7:30 pm - 9:30 pm Drug Design, Docking

7:30 pm - 7:45 pm Discussion leader: Dr. Peter W. Kenny (AstraZeneca, Cheshire, United Kingdom)

7:45 pm - 8:15 pm Dr. Andrew Leach (GlaxoSmithKline Med. Res. Centre, Stevenage, United Kingdom)
"Virtual screening: theory and practice"

8:15 pm - 8:25 pm Discussion

8:25 pm - 8:55 pm Dr. Terry Stouch (J. Computer-Aided Molecular Design, USA)
"Drug design, water, and solvation"

8:55 pm - 9:05 pm Discussion

9:05 pm - 9:25 pm Dr. Andreas H. Goeller (Bayer HealthCare AG, Wuppertal, Germany)
"Modelling protein-mediated oxidation of small molecules: A mixed quantum-mechanics and descriptor-based approach"

9:25 pm - 9:30 pm Discussion

9:30 pm - ... Bar, Poster Session

WEDNESDAY, 11 October 2006

7:30 am - 8:30 am Breakfast

9:00 am - 12:30 pm Searching, Electrostatics, Free Energy

9:00 am - 9:15 am Discussion leader: Dr. Philippe H. Hunenberger (ETH Zurich, Zurich, Switzerland)

9:15 am - 9:45 am Prof. Andrew E. Torda (University of Hamburg, Germany)
"Statistical scoring functions - not haunted by the ghost of Herrn Boltzmann"

9:45 am - 10:00 am Discussion

10:00 am - 10:30am Coffee break

10:30 am - 11:00 am Prof. Paul Tavan (Ludwig-Maximilian University Munich, Germany)
"Electrostatics of proteins in solvent continua: Newtons third law marries qE-forces. A progress report"

11:00 am - 11:15 am Discussion

11:15 am - 11:45 pm Prof. Johan Aqvist (University of Uppsala, Uppsala, Sweden)
"Free energy calculations on the ribosome"

11:45 am - 12:00 am Discussion

12:00 pm - 12:20 pm Dr. Chris Oostenbrink (Free University of Amsterdam, Amsterdam, The Netherlands)
"Efficient free energy calculations from biomolecular simulations: Methodology and applications"

12:20 pm - 12:30 pm Discussion

12:30 pm Campaign speeches and election

1:00 pm Lunch

6:00 pm - 7:30 pm Dinner

7:30 pm - 9:30 pm Coarse-Graining

7:30 pm - 7:45 pm Discussion leader: Dr. Bojan Zagrovic (ETH Zurich, Zurich, Switzerland)

7:45 pm - 8:15 pm Dr. Julian C. Shillcock (Max-Planck-Institute, Potsdam, Germany)
"Mesoscopic simulations of actin filaments, lipid vesicles and nanoparticles"

8:15 pm - 8:25 pm Discussion

8:25 pm - 8:55 pm Prof. Siewert-Jan Marrink (University of Groningen, Groningen, The Netherlands)
"Membrane proteins in action"

8:55 pm - 9:05 pm Discussion

9:05 pm - 9:25 pm Dr. Christine Peter (Max-Planck-Institute, Mainz, Germany)
"Multiscale modeling of photoactive liquid crystalline systems"

9:25 pm - 9:30 pm Discussion

9:45 pm - ... Bar, Poster Session

THURSDAY, 12 October 2006

7:30 am - 8:30 am Breakfast

9:00 am - 12:30 pm Applications, Membranes

9:00 am - 9:15 am Discussion leader: Prof. David Beveridge (Wesleyan University, Connecticut, USA)

9:15 am - 9:45 am Dr. Gerhard Hummer (National Institutes of Health, Bethesda, USA)
"Protein dynamics: From nanoseconds to microseconds and beyond"

9:45 am - 10:00 am Discussion

10:00 am - 10:30am Coffee break

10:30 am - 11:00 am Prof. Benoit Roux (University of Chicago, Chicago, USA)
"Computation of absolute (standard) binding free energies"

11:00 am - 11:15 am Discussion

11:15 am - 11:45 pm Prof. Olle Edholm (Royal Institute of Technology, Stockholm Sweden)
"Monitoring long time dynamic processes in lipid bilayers by molecular dynamics simulations"

11:45 am - 12:00 am Discussion

12:00 pm - 12:20 pm Dr. Yuji Takaoka (Taisho Pharmaceutical Co., Saitama, Japan)
"Molecular dynamics simulation of phospholipid bilayer membrane under hydrostatic pressure control and surface tension"

12:20 pm - 12:30 pm Discussion

12:30 pm Lunch

4:00 pm - 6:00 pm Poster Session

6:00 pm - 7:30 pm Dinner

7:30 pm - 9:30 pm Quantum Dynamics

7:30 pm - 7:45 pm Discussion leader: Dr. Bill Swope (IBM, San Jose, USA)

7:45 pm - 8:15 pm Dr. Irene Burghardt (Ecole Normale Superieure, Paris, France)
"Photochemistry and non-adiabatic quantum dynamics: Multiconfigurational methods and effective-mode models for large systems"

8:15 pm - 8:25 pm Discussion

8:25 pm - 8:55 pm Dr. Sara Bonella (University of Rome, La Sapienza, Italy)
"Mixed quantum classical dynamics for systems with many degrees of freedom: Linearization methods and time correlation functions"

8:55 pm - 9:05 pm Discussion

9:05 pm - 9:25 pm Yolanda A. Small (The Pennsylvania State University, Pennsylvania, USA)
"Hydrogen bonding pathways and hydrogen transfer in dihydrorotate dehydrogenase"

9:25 pm - 9:30 pm Discussion

9:30 pm - ... Bar, Poster Session

FRIDAY, 13 October 2006

7:30 am - 8:30 am Breakfast

9:00 am Departure


Pre-registered Posters 2006

Many of these posters had co-authors; these were not listed in the program.

Poster Group A

1. Elena Akhmatskaya, Fujitsu Laboratories of Europe
Targeted Shadowing Hybrid Monte Carlo: A Novel Approach for Biomolecular Simulation.

2. Urban Borstnik, National Institute of Chemistry
Load Balancing in the force Decomposition Method for Parallelizing Molecular Dynamics.

3. Clara Christ, ETH Zurich
Efficient calculation of free energy differences between multiple states.

4. John Daily, University of Colorado
To be announced.

5. Delos DeTar, Florida State University
Calculation of Entropy.

6. Elisa Fadda, The Hospital for Sick Children
QM/MM Free Energy Study of Proton Transport in Protein Channels.

7. Franca Fraternali, King's College
Dynamics and orientation of fluorescent probes attached to the C-terminal region of TNI.

8. Andreas Goeller, Bayer Healthcare AG
Outperforming Classical Modelling by Aid of Quantum Chemistry.

9. Ming-Hong Hao, Boehringer Ingelheim Pharmaceuticals, Inc.
Theoretical Calculation of the Hydrogen Bonding Strength of Drug Molecules.

10. Hans Horn, IBM Almaden Research Center
Organocatalytic Ring Opening Polymerization of L-Lactide: A mechanism involving a hydrogen bonded or covalently bound guanidine based catalyst?

11. Petra Imhof, University Heidelberg
Exploring the photo-induced green-to-red conversion of fluorescent protein EosFP.

12. Peter Kasson, Stanford University
Ensemble simulation of membrane fusion: Fusion mechanism controlled by lipid composition.

13. Janez Konc, National Institute of Chemistry Slovenia
Predicting protein interactions with surface descriptors.

14. Hans Georg Limbach, Nestec S.A.
Simulations of Carbohydrate Water Mixtures.

15. Jeremy Moix, Georgia Institute of Technology
Molecular Dynamics and Stochastic Simulations of Surface Diffusion.

16. Maria Nagan, Truman State University
Molecular Dynamics Studies Examining the Role of Nonstandard Bases in RNA Recognition.

17. Alexandra Patriksson, Uppsala University
Proteins under electrospray conditions: a simulation study.

18. Maria Reif, Swiss Federal Institute of Technology Zurich
Ionic solvation: Ion-water Lennard-Jones potentials based on accurate hydration free energies from classical MD simulation.

19. Jurgen Schlitter, University of Bochum
The induced fit of an enzyme substrate in IR spectra and QM/MM simulations.

20. Hans Martin Senn, Max Planck Institute for Coal Research
Insight into enzymatic C-F and C-Cl bond formation from QM and QM/MM calculations.

21. Motoyuki Shiga, Japan Atomic Energy Agency
Accelerating QM/MM molecular dynamics using multiple-time-scale approach combined with perturbation theory.

22. Terry Stouch, Journal of Computer-Aided Molecular Design
Explicit and implicit solvation of protein / drug binding sites.

23. Matthew Tessier, University of Georgia
Lipid Simulations using GLYCAM 06.

24. Nico Van Der Vegt, Max-Planck-Institute for Polymer Research
Multiscale modeling of biomolecules close to metal surfaces.

25. Robert Woods, University of Georgia
Latest Advances in Carbohydrate force Field (GLYCAM) Development and Experimental Validation: Polarizability and TIP5P-Consistency.

Poster Group B

26. Alessio Amadasi, University of Parma
Towards a virtual screening that includes protein flexibility: the case study of the estrogen receptor.

27. Donald Boyd, IUPUI
Conformational Analysis of a Bioactive Polymer Using a Monte Carlo Method.

28. Gerardo Cisneros, Nat. Inst. of Environmental Health Science
Generalization of the density fitting based Gaussian Electrostatic Model: Extension to arbitrary angular moment, distributed multipoles and computational speedup.

29. Jonas Danielsson, University of Basel
Reactive molecular dynamics on multiple electronic surfaces.

30. Jozica Dolenc, University of Ljubljana
Free energies of netropsin binding to a number of DNA binding sequences.

31. Francesca Fanelli, University of Modena and Reggio Emilia
Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling.

32. Simone Fulle, J.W. Goethe-University
Investigation of the dynamical aspects of the ribosomal exit tunnel.

33. Alan Graves, UCSF
Pushing the boundaries of molecular docking with decoys and model systems.

34. Richard Henchman, University of Manchester
Solvent free energy from a single simulation via cell theory.

35. Dragos Horvath, CNRS
Steps towards an ensemble-based force field fitting procedure.

36. Frank Jensen, SDU
QM and MM conformational analysis of amino acids.

37. Bettina Keller, ETH Zurich
On using oscillating time-dependent restraints in MD simulation.

38. Krzysztof Kuczera, University of Kansas
Modeling the hinge-bending motion in S-adenosyl-L-homocysteine hydrolase.

39. Mark Mackey, Cresset Biomolecular Discovery
Eliminating the need for X-ray structures: using ligand data to derive the size, shape and nature of a protein binding site.

40. Luca Monticelli, University of Calgary
Aggregation of Peptides in a Lipid Bilayer: Insights from MD Simulations with a Coarse-Grained Model.

41. Elena Olkhova, Max Planck Institute of Biophysics
Multiconformation Continuum Electrostatics Analysis of the NhaA - Na+/H+ Antiporter of Escherichia coli with Functional Implications.

42. Eric Patterson, Truman State University
Mechanisms of Nucleophilic Displacements in Phosphonothiolates.

43. Markus Reiher, ETH Zurich
Calculation and Interpretation of Vibrational Raman Optical Activity Spectra for Polypeptides.

44. Franziska Schmid, University of Basel
Atomistic study of feedback inhibition in guanylate cyclase pled.

45. Jufang Shan, St. Jude Children's Research Hospital
Discovery and Computational Co-crystallization of Novel Inhibitors of the Dishevelled PDZ Domain.

46. Michael Shirts, Columbia University
The importance of conformational sampling in precise calculations of FKBP12 ligand binding affinity.

47. William Swope, IBM Research
Describing the folding of a lambda(6-85) mutant using replica exchange molecular dynamics.

48. Andrew Torda, University of Hamburg
Protein score functions, optimisation and optimism.

49. Junmei Wang, Encysive Pharmaceuticals Inc.
Development of a Universal AMBER force Field.

50. Huafeng Xu, D. E. Shaw Research LLC
pKa Calculations by Free Energy Simulations in Explicit Solvent.

Poster Group C

51. Simon Berneche, Swiss Institute of Bioinformatics, Universite de Lausanne
Assessment of Water Molecules Stability in the Pore of the AmtB Channel.

52. Jens Carlsson, Uppsala University
Estimation of binding free energies for nonnucleoside inhibitors of HIV-1 reverse transcriptase using the linear interaction energy method.

53. Vlad Cojocaru, EML Research GGMBH
The Ins and Outs of Cytochromes P450.

54. Leonardo De Maria, Novozymes A/S
Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modelling.

55. Ron Dror, D. E. Shaw Research
Novel Algorithms for Scalable Molecular Dynamics Simulations on Commodity Clusters.

56. Reinhold Fink, University of Wuerzburg
Retaining the excitation degree perturbation theory: A well defined multi-reference configuration electron structure method.

57. Zrinka Gattin, ETH Zurich
Influence of missing hydrogen bonds on the stability of beta-peptides.

58. Nohad Gresh, Centre National De La Recherche Scientifique
Application of polarizable molecular mechanics to study the complexes of inhibitors with the Zn-metalloenzyme phosphomannoisomerase.

59. Berk Hess, Max-Planck Institute for Polymer Research
Effective potentials for ions in solution.

60. Jozef Hritz, Vrije Universiteit
Soft atoms: Computational protein structure through unphysical sampling.

61. Johannes Kaestner, CCLRC Daresbury Lab
Umbrella integration: A novel analysis method for umbrella sampling simulations.

62. Peter W. Kenny, AstraZeneca
Automated molecular editing: Ionization, tautomers & matched molecular pairs.

63. Robert LaTour, Clemson University
Replica-Exchange Molecular Dynamics Simulations of Protein Adsorption Behavior.

64. Colin McMartin, Thistlesoft
Learning from high resolution protein XRAY structures.

65. Samuel Moors, University of Leuven
Tryptophan Rotamers and Native-State Dynamics Studied by Molecular Dynamics Modeling.

66. Chris Oostenbrink, Vrije Universiteit
Efficient calculation of binding free energies.

67. Christine Peter, Max Planck Institute for Polymer Research
Multiscale modeling of photoactive systems.

68. Ute Roehrig, Ludwig Institute of Cancer Research
Docking Study of Indoleamine 2,3-Dioxygenase Ligands.

69. Michael Schnieders, Washington University
Polarizable Multipole Solutes in Continuum Solvent.

70. Yihan Shao, Q-Chem Inc.
The development of QM/MM models within the Q-Chem software package.

71. Yolanda Small, Pennsylvania State University
Theoretical studies of proton and hydride transfer reactions catalyzed by dihydroorotate dehydrogenase.

72. Yuji Takaoka, Taisho Pharmaceutical Co., Ltd.
Extended methods of molecular dynamics simulations under hydrostatic pressure and surface tension: Application to a hydrated DMPC bilayer.

73. Tell Tuttle, Max-Planck-Institut fur Kohlenforschung
The Binding of Latrunculin and Synthetic Analogs to Actin: A QM/MM MD Study.

74. Moritz Winger, ETH Zurich
MD simulation of IL4 under neutral and low pH: With a note on the effect of conterions on the stability of proteins.

75. Bojan Zagrovic, ETH Zurich
Helical signature motif in the fiber diffraction patterns of random-walk chains.

Poster Group D

76. Regine Bohacek, Boston De Novo Design
Protein flexibility observed.

77. John Chodera, University of California, San Francisco
Folding kinetics of the engineered peptide trpzip2 from master equation models constructed from atomistic simulation.

78. Michel Cuendet, EPFL
A Steered Molecular Dynamics Study of the T Cell Receptor - Peptide - MHC complex.

79. Daniele Dell'orco, University of Modena and Reggio Emilia
Computational screening of mutational effects on protein-protein and protein-DNA interactions: A fast docking-based approach.

80. Bernd Engels, University Wurzburg
Gradient Tabu Search.

81. Antony Fouqueau, University of Basel
Adsorption of Acridine Orange at C_18/water/acetonitrile interface.

82. Daan Geerke, van Gunsteren Group, ETH
The Use of Polarizable force Fields in Molecular Dynamics Simulations of Liquid Ethylene Glycol and its Aqueous Mixtures.

83. Victor Guallar, Washington University School of Medicine
PELE (microsecond protein dynamics) and QM/MM.

84. Ronald Hills, Scripps Research Institute
Exploring folding landscapes with a flavored go model.

85. Hao Hu, Duke University
Simulating the QM/MM Free Energy Reaction Path of Reactions in Enzymes and Solutions.

86. Kalju Kahn, University of California, Santa Barbara
Basis set extrapolation: Principles and applications to biomolecules.

87. Barbara Kirchner, University of Bonn
Introducing a consistent relativistic description into simulations: Combining second order Douglas-Kroll-Hess theory with first-principles simulations.

88. Jessica Liberles, University of Bergen
Detecting distant homologs within a superfold.

89. David Mobley, University of California, San Francisco
Predictive absolute binding free energies for an engineered binding site.

90. Yuguang Mu, Nanyang Technological University
Molecular Dynamics of Minicircular Duplex DNA.

91. Nikolaj Otte, Max-Planck-Institute for Coal Research
Enantioselectivity of Enzymatic Ester Hydrolysis: A QM/MM Study.

92. Jed Pitera, IBM Research
On the convergence of replica-exchange molecular dynamics simulations in explicit solvent: The trpzip2 beta-hairpin peptide in water.

93. Edina Rosta, University of Southern California
Studies of the Reaction Mechanism of Phosphate Hydrolysis in the Ras-GAP Proteins and in Aqueous Model Systems.

94. Verena Schultheis, University of Munich
Extracting Markov models of peptide conformational dynamics from simulation data.

95. Shenghua Shi, Plexxikon Inc.
Constrained docking for scaffold-based drug discovery.

96. Harry Stern, University of Rochester
Constant pH simulation with explicit solvent - direct approach from the semigrand ensemble.

97. Hepan Tan, Columbia University
Structure Based Design of HIV-1 Entry Inhibitors.

98. David Van Der Spoel, Uppsala University
Protein Folding Properties from Molecular Dynamics Simulations.

99. Cynthia Woodbridge, Hillsdale College
Ab Initio modeling of the vibrational spectra of adsorbed metallocenes and fragments.

100. Yingkai Zhang, New York University
Ab initio QM/MM Studies of Histone Modifying Enzymes.


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