Gordon Research Conference
New Computational Tools For 21st Century Chemistry

July 27 - August 1, 2008
Mount Holyoke College
South Hadley, MA

Chair: Jed W. Pitera
Vice Chair: Walter Thiel

PROGRAM (with last-minute revisions)

Journal of Chemical Theory and Computation
Springer, publisher of Journal of Computer-Aided Molecular Design
Chemical Computing Group

SUNDAY, July 27, 2008

2:00 pm - 11:00 pm Arrival and Check-in

6:00 pm Dinner

7:30 pm - 7:40 pm Welcome / Introductory Comments by GRC Site Staff

7:40 pm - 8:30 pm Keynote Session: Simulating Rates of Biological Processes
Discussion Leader: Jed W. Pitera (IBM Research)

7:40 pm - 8:20 pm J. Andrew McCammon (UCSD)
"Rate Processes in Biophysics: From the Molecule to the Cell"
8:20 pm - 8:40 pm Discussion

8:40 pm - 9:30 pm Biomolecular Electrostatics I
Discussion Leader: Darrin York (U. Minnesota)

8:40 pm - 9:15 pm Nathan Baker (Washington University - St. Louis)
"Assessing the performance of continuum models for nonpolar solvation"
9:15 pm - 9:30 pm Discussion

9:30 pm - 10:30 pm Reception


7:30 am - 8:30 am Breakfast

8:45 am Group Photo

9:15 am - 12:30 pm Biomolecular Electrostatics II
9:15 am - 9:35 am Discussion Leader: Darrin York (U. Minnesota)

9:45 am - 10:10 am Jana Khandogin (U. Oklahoma)
"Electrostatic interactions in the unfolded states of proteins"
10:10 am - 10:20 am Discussion

10:20 am Coffee Break

10:50 am - 11:25 am Matt Jacobson (University of California, San Francisco)
"Electrostatic switches in proteins"
11:25 am - 11:40 am Discussion

11:40 am - 12:15 pm Luigi Delle Site (MPI-Polymers, Mainz)
"The Adaptive Resolution Simulation Scheme (AdResS): Basic Principles and Applications"
12:15 pm - 12:30 pm Discussion

12:30 pm Lunch

1:30 pm - 4:00 pm Free Time

4:00 pm - 6:00 pm Poster Session A

6:00 pm Dinner

7:30 pm - 9:30 pm Open Boundary Multiscale Modelling
7:30 pm - 7:45 pm Discussion Leader: William Swope (IBM Research)

7:45 pm - 8:10 pm Donald Truhlar (U. Minnesota)
"Open Boundary approaches for QM/MM calculations"
8:10 pm - 8:20 pm Discussion

8:20 pm - 8:45 pm Bernd Ensing (U. Amsterdam)
"Construction of an adaptive atomistic / coarse-grained molecular dynamics method"
8:45 pm - 8:55 pm Discussion

8:55 pm - 9:20 pm Celeste Sagui (NCSU)
"Accurate electrostatics for organic molecules"
9:20 pm - 9:30 pm Discussion


7:30 am - 8:30 am Breakfast

9:00 am - 12:30 pm Statistics and Sampling
9:00 am - 9:20 am Discussion Leader: David Kofke (SUNY-Buffalo)

9:20 am - 9:55 am Wei Yang (Florida State University)
"Quantitative Alchemical Free Energy Simulations: Are We There Yet?"
9:55 am - 10:10 am Discussion

10:10 am Coffee Break

10:30 am - 11:10 am Aaron Dinner (University of Chicago)
"Automated analysis of path sampling simulations reveals a mechanism for DNA damage detection"
11:10 am - 11:25 am Discussion

11:25 am - 12:15 pm Daniel Zuckerman (University of Pittsburgh)
"A blind, automated procedure for estimating the effective sample size of a molecular simulation"
12:15 pm - 12:30 pm Discussion

12:30 pm Lunch

1:30 pm - 4:00 pm Free Time

4:00 pm - 6:00 pm Poster Session A

6:00 pm Dinner

7:30 pm - 9:30 pm Advances in Quantum Chemistry
Discussion Leader: Walter Thiel (MPI-MŸlheim)

7:30 pm - 8:00 pm Takao Tsuneda (U. Tokyo)
"Long-range corrected density functional theory and its progress"
8:00 pm - 8:10 pm Discussion

8:10 pm - 8:40 pm Julia Rice (IBM Research)
"A unified theory of periodic boundary condition QM/MM"
8:40 pm - 8:50 pm Discussion

8:50 pm - 9:20 pm Valentino Cooper (Rutgers)
"Applications of the van der Waals density functional: DNA and metal organic framework materials"
9:20 pm - 9:30 pm Discussion


7:30 am - 8:30 am Breakfast

9:00 am - 12:30 pm Advances in (Bio)molecular Simulation
9:00 am - 9:20 am Discussion Leader: Alan Grossfield (U. Rochester)

9:20 am - 9:55 am Terry P. Lybrand (Vanderbilt)
"Molecular simulation of cyclooxygenase-inhibitor complexes: Insights into inhibitor binding and selectivity"
9:55 am - 10:10 am Discussion

10:10 am Coffee Break

10:30 am - 11:10 am Juan de Pablo (University of Wisconsin, Madison)
"Coarse Grain Simulations of Complex Materials - Polymers, Copolymers and Liquid Crystals"
11:10 am - 11:25 am Discussion

11:25 am - 12:15 pm Modesto Orozco (IRB Barcelona)
"From atomistic to genomic scale simulations"
12:15 pm - 12:30 pm Discussion

12:30 pm Lunch

1:30 pm - 4:00 pm Free Time

4:00 pm - 6:00 pm Poster Session B

6:00 pm Dinner

7:30 pm - 9:30 pm Industrial Applications of Computational Chemistry
7:30 pm - 7:45 pm Discussion Leader: Terry Stouch (Springer/JCAMD)

7:45 pm - 8:20 pm Theresa Johnson (Pfizer)
"Data, data everywhere and not a drop of information: Leveraging high quality internal kinase data into usable information"
8:20 pm - 8:30 pm Discussion

8:30 pm - 9:05 pm Alice Glaettli (BASF)
"Molecular Modelling for Crop Protection"
9:05 pm - 9:20 pm Discussion


7:30 am - 8:30 am Breakfast

9:00 am - 12:30 pm Computation of Spectroscopic Observables
9:00 am - 9:10 am Discussion Leader: Jed Pitera (IBM Research)

9:10 am - 9:50 am Alexei Stuchebrukhov (University of California, Davis)
"Computational studies of redox-driven proton pump cytochrome c oxidase"
9:50 am - 10:05 am Discussion

10:05 am Coffee Break

10:35 am - 10:55 am Stefano Tonzani (Northwestern University)
"A practical approach for DNA spectra and dynamics in solution"
10:55 am - 11:05 am Discussion

11:05 am - 11:25 am Deniz Sezer (MPI-Biophysics)
"Calculation of ESR spectra from MD simulations"
11:25 am - 11:35 am Discussion

11:35 am - 12:15 pm Andrei Tokmakoff (MIT)
"Simulations of the Infrared Spectroscopy of Water and Proteins"
12:15 pm - 12:30 pm Discussion

12:30 pm Lunch

1:30 pm - 4:00 pm Free Time

4:00 pm - 6:00 pm Poster Session B

6:00 pm Dinner

7:00 pm - 7:30 pm Business Meeting
(Fill out Conference Evaluation Forms; Discuss future Site & Scheduling preferences)

7:30 pm - 9:30 pm Physical Methods in Docking and Drug Discovery
Discussion Leader: Michelle Lamb (Astra-Zeneca)

7:30 pm - 8:10 pm Geoff Skillman (Openeye)
"SAMPL: A true(r) test of modeling"
8:00 pm - 8:10 pm Discussion

8:10 pm - 8:40 pm Iris Antes (MPI-Informatik)
"Inclusion of protein flexibility in molecular docking"
8:40 pm - 8:50 pm Discussion

8:50 pm - 9:20 pm B. Woody Sherman (Schrodinger)
"Accurate treatment of protein flexibility, polarized charges, and explicit waters in docking and scoring"
9:20 pm - 9:30 pm Discussion


7:30 am - 8:30 am Breakfast

9:00 am Departure

2008 Computational Chemistry Gordon Research Conference - Poster List
Chair: Jed W. Pitera

Planned presenters of pre-registered posters are listed below. Coauthors of poster papers were not included in the program.

Set A: Displayed Monday and Tuesday

A1. ANANDAKRISHNAN, R. (VIRGINIA TECH) - Multilevel charge approximation based on the natural organization of biomolecules for speeding up electrostatic computations

A2. BAO, X. (OHIO STATE UNIVERSITY) - Spin Trapping of Hydroperoxyl Radical by a Cyclic Nitrone Conjugated to Cyclodextrin: A Computational Study

A3. BERCES, A. (CHEMISTRY LOGIC) - Implementation of Cheminformatics Methods on Reconfigurable Computers

A4. BOYD, D. (IND. UNIV. - PURDUE UNIV. - INDIANAPOLIS) - Current Trends in the Job Market for Computational Chemists

A5. CERUTTI, D. (VANDERBILT UNIVERSITY) - Protein Simulations in the Crystal and Solution Phases: New Prospects for Atom-Level Simulations

A6. CHATFIELD, D. (FLORIDA INTERNATIONAL UNIVERSITY) - Theoretical study of chloroperoxidase: (1) Enantiospecifity of catalytic epoxidation, (2) Mechanism of catalytic halogenation

A7. CLICK, T. (CENTRAL MICHIGAN UNIVERSITY) - Calculation of pKa's for positively-charged amino acids using a polarizable force field

A8. DECORNEZ, H. (AMRI) - Development of a generalized kinase docking model

A9. DROR, R. (D. E. SHAW RESEARCH) - Anton: A special-purpose machine enabling millisecond-scale molecular dynamics simulations

A10. FAN, H. (UNIVERSITY OF CALIFORNIA, SAN FRANCISCO) - Virtual Ligand Screening Using Comparative Models of Proteins

A11. FRIGERIO, F. (ENI R&M) - Molecular Modelling of Diesel Engine Soot Dispersants

A12. GOUMANS, T. (UNIVERSITY COLLEGE LONDON) - Embedded cluster calculations of astrochemistry on surfaces

A13. GROSSFIELD, A. (U. ROCHESTER MED CTR) - LOOS: An extensible platform for structural analysis of simulations

A14. HO, B. (UCSF) - Generating large conformational changes in proteins using local perturbations

A15. IMHOF, P. (UNIVERSITY OF HEIDELBERG) - Transition Networks for Modelling Enzymatic Catalysis

A16. JOUNG, I.S. (UNIVERSITY OF UTAH) - Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

A17. KRILOV, G. (BOSTON COLLEGE) - Efficient non-periodic dynamic boundary solvation models for biomolecular simulations

A18. LEE, S. (UNIVERSITY OF FLORIDA) - Low frequency motions in Formyl-CoA Transferase. A normal mode analysis

A19. LI, G. (BIOGEN-IDEC) - Kinase flexibility

A20. LIN, P. (THE PENNSYLVANIA STATE UNIVERSITY) - Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase §

A21. LOEFFLER, H. (STFC DARESBURY LABORATORY) - Coarse-Grained Force Fields applied to Biomolecules: using the MARTINI force field to extend simulations of EGFR

A22. MCKAY, D. (MERCK FROSST) - Charge-ELF: addressing conformational dependency of small-molecule atomic charges for biomolecular simulations

A23. NAM, K. (HARVARD UNIVERSITY) - Free energy simulation studies of the molecular mechanism of the specific damaged base recognition by MutM

A24. NILAR, S. (NOVARTIS INST. FOR TROPICAL DISEASES) - A Data Mining Triage for the Selection of Chemically Interesting Scaffolds from High Throughput Screening Assays for the Dengue Virus.

A25. PANDIT, D. (EXSAR CORPORATION) - Correlating H/D Exchange and Molecular Dynamics Simulations

A26. PEARCE, B. (BRISTOL-MYERS SQUIBB CO.) - E-Novo Automated Workflow for Structure-Based Lead Optimization

A27. PHAM, N. (UNIVERSITY OF UTAH) - Kinetic Modeling of the Epoxy-Amine Curing Reaction

A28. REN, P. (UNIVERSITY OF TEXAS AT AUSTIN) - Free Energy Simulation of Protein-Ligand Binding with Polarizable Potential

A29. ROSSO, L. (IMPERIAL COLLEGE) - Non-Specific Binding of Positron Emission Tomography (PET) Ligands as Seen from Ab-initio Computational Study

A30. SALAZAR, P. (TEXAS A&M UNIVERSITY) - A novel descriptor for the analysis of binding affinity in drug design based on an ab-initio approach

A31. SCHMIEDEKAMP, A. (PENN STATE UNIVERSITY, ABINGTON) - Artificial DNA metallo-base pairs: rationale for metal selectivity in Ni(II)-binding purine-like base pair

A32. SHIRTS, M. (COLUMBIA UNIVERSITY) - Converging ligand binding calculations using Folding@Home: FKBP and Factor Xa

A33. SMITH, D. (UNIVERSITY OF PITTSBURGH) - Self-Guided Dynamics: A Critical Review

A34. STERN, H. (UNIVERSITY OF ROCHESTER) - Studies on binding affinity calculations


A36. SWOPE, W. (IBM RESEARCH) - Explicit solvent solvation free energies for over 100 small molecules with drug-like functionality

A37. TAN, L. (UNIVERSITY OF BONN) - Integrating Approaches of Molecular Docking and Similarity Search Calculations on Multiple Targets in Virtual Screening

A38. TONZANI, S. (NORTHWESTERN UNIVERSITY) - A practical approach to DNA structure, spectra and dynamics

A39. ULMSCHNEIDER, J. (UNIVERSITY OF OXFORD) - Folding membrane proteins in implicit membrane models

A40. WENZEL, W. (FORSCHUNGSZENTRUM KARLSRUHE) - High Throughput In Silico Screening with Receptor Flexibility

A41. WU, C. (WASHINGTON UNIVERSITY) - Extension of the AMOEBA Force Field to Nucleic Acids

A42. XU, J. (OAK RIDGE NATIONAL LAB) - Association and Interaction of Cohesin-dockerin Complex in Cellulosome Assembly

A43. ZHAO, Y. (UNIVERSITY OF MINNESOTA) - NMR shielding constants with meta-GGA

Set B: Displayed Wednesday and Thursday

B44. BANDYOPADHYAY, D. (GLAXOSMITHKLINE) - Geometric models of uncertainty: Applications for robust target flexibility analysis and function prediction in computational chemistry

B45. BARVIK, I. (CHARLES UNIVERSITY, INSTITUTE OF PHYSICS) - Homology Modeling and Molecular Dynamics Simulations of RNA Polymerases

B46. BOYD, D. (IND. UNIV. - PURDUE UNIV. - INDIANAPOLIS) - Shape and Charge Distribution Study of a Polymer that inhibits HIV-1 Reverse Transcriptase Activities


B48. CHANG, C. (UNIVERSITY OF CALIFORNIA, RIVERSIDE) - Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association

B49. CHENG, Y. (UNIVERSITY OF CALIFORNIA, SAN DIEGO) - Finite Element Analysis of Biomolecular electrostatics and diffusion with the SMOL package

B50. DAMJANOVIC, A. (JOHNS HOPKINS UNIVERSITY) - Backbone relaxation coupled to the ionization of internal groups in proteins: A self-guided Langevin dynamics study.

B51. DOMRACHEVA, T. (MAX PLANCK INSTITUTE FOR MEDICAL RESEARCH) - Quantum-chemical analysis of the primary processes in BLUF photosensors


B53. FLORIAN, J. (LOYOLA UNIVERSITY CHICAGO) - Calculations of dNTP binding contributions to DNA polymerase fidelity

B54. GOREN, A. (TRANSYLVANIA UNIVERSITY) - Computational Study of Group15 (X) and Group 16 (Y) Trimer Cations, (X3Y3)+

B55. GRESH, N. (CNRS, FRANCE) - Polarizable molecular mechanics studies of inhibitor binding to Fak kinase

B56. GUNNER, M. (CITY COLLEGE OF NEW YORK) - Modifying Continuum Electrostatics to calculate pKas and Ems accurately

B57. HODOSCEK, M. (NATIONAL INSTITUTE OF CHEMISTRY) - Parallel/Parallel methods in the CHARMM Program

B58. IRLE, S. (NAGOYA UNIVERSITY) - DFTB/MD simulations of SWNT growth on Fe nanoparticles

B59. KOZAKOV, D. (BOSTON UNIVERSITY) - Efficient protein docking algorithm using Generalized Fourier Transforms

B60. LATOUR, R. (CLEMSON UNIVERSITY) - Temperature Intervals with Global Exchange of Replicas (TIGER) - A More Efficient REMD Method

B61. LEONARD, J. (CHEMICAL COMPUTING GROUP) - Generating novel, structurally-constrained compounds from a set of known ligands

B62. LIMBACH, H.J. (NESTLE RESEARCH CENTER) - Small Molecules at the Ice Water Interface

B63. LIN, Y. (UNIVERSITY OF HELSINKI) - Experimental and Computational Studies of Alkali-Metal Coinage-Metal Clusters

B64. LYMAN, E. (CENTER FOR BIOPHYSICAL MODELING AND SIMULATION) - Contact topology and the spectrum of normal modes

B65. MOUSTAKAS, D. (HARVARD UNIVERSITY) - Rule-based modeling of antibody oligomerization

B66. NICHOLS, S. (YALE UNIVERSITY) - Hierarchical screening with multiple receptor structures to target the non-nucleoside binding site of HIV-1 reverse transcriptase

B67. ORTIZ, V. (UNIVERSITY OF WISCONSIN-MADISON) - Sequence-dependent mechanical properties of DNA and their implication in assembly

B68. PARANDEKAR, P. (INDIANA UNIVERSITY) - QM/QM Electronic Embedding Models for Materials Chemistry


B70. PONDER, J. (WASHINGTON UNIVERSITY MEDICAL SCHOOL) - Extension of the AMOEBA Polariizable Force Field to Nucleic Acids

B71. ROOKLIN, D. (NYU) - Protein Tyrosine Phosphatase 1B: Resolving the Wild-Type Mechanism with ab initio QM/MM Molecular Dynamics Simulations

B72. RYDBERG, P. (COPENHAGEN UNIVERSITY) - Using DFT to improve prediction of drug metabolism

B73. SAMBRISKI, E. (UNIVERSITY OF WISCONSIN-MADISON) - Directed Assembly of DNA at the Nanoscale: Model and Applications

B74. SEZER, D. (MAX PLANCK INSTITUTE OF BIOPHYSICS) - Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations


B76. SONG, Y. (CCNY) - Applications of Multi-Conformation Continuum Electrostatics beyond pKa predictions

B77. STOTE, R. (CNRS) - An MM/PBSA study of Bcl-2 family protein interactions

B78. SUKUMAR, N. (RENSSELAER POLYTECHNIC INSTITUTE) - Molecular Descriptors for Biological Systems

B79. TAN, H. (HARVARD UNIVERSITY) - Structural Flexibility and Rigidity Analysis of HIV-1 gp120

B80. TE, J. (GEORGETOWN UNIVERSITY) - Soft-sticky approximate moment expansion: a potential energy function for coarse-grained molecules

B81. TSAI, I. (CITY UNIVERSITY OF NEW YORK-HUNTER COLLEGE) - Optimized Collagen-Like Triple Helix by Density Functional Theory

B82. WANG, S. (QUEEN'S UNIVERSITY) - The chirality transfer from chiral solutes and surfaces to achiral solvents


B84. XIAO, Y. (TARGACEPT INC.) - The role of different regions in the binding site of the alpha 7 Neuronal Nicotinic Receptor

B85. ZHAO, C. (QUEEN'S UNIVERSITY) - Mechanism and Optimization of a Chiral Stationary Phase: A Molecular Dynamics Study

B86. ZHENG, Z. (CITY COLLEGE, CUNY) - Analysis of the electrochemistry and coupled protonation of hemes with Ems spanning 800 mV

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