COMPTuesday, 30 August 2005

6:00 PM-8:00 PM Washington DC Convention Center -- Hall A, Poster
Poster Session -- Sponsored by Novartis Institutes for BioMedical Research
Organizer:Wendy D. Cornell
Electron paramagnetic resonance and equilibrium atomic configurations studies of binuclear niobium molecules in Li-Nb phosphate glass dielectrics
Sabrina A. Arrington-Peet, Rakhim R. Rakhimov, Vladimir I. Gavrilenko
Novel docking and scoring approach to rank-ordering compounds by potency
Xuan Hong, Scott Kahn, C. M. Venkatachalam, Chaya Duraiswami, Catherine E. Peishoff, Martha S. Head
Paper Withdrawn
Application of Swarm algorithm for efficient in silico screening of chemical database
Lei Wang, J. Graham, John O. Trent
Dynamics of single-substrate continuous cultures: An integrated model of bacterial cell
Shakti Gupta, Sergei S. Pilyugin, Atul Narang
On the use of suffix trees in multiple sequence alignment
Kal Renganathan Sharma
Parallel computing in the undergraduate chemistry curriculum
Khamis Siam
Q-Chem 3.0: More chemistry, faster
Jing Kong
QSPR analysis of solvent effect on selectivity of 18-crown-6 between Nd3+ and Eu3+ ions: A Monte Carlo simulation study
Hag Sung Kim
QSPR analysis on selectivity of between K+ and Na+ ions to 12-Crown-4: A Monte Carlo simulation study
Hag Sung Kim
Solid state DFT methods and the property prediction of energetic materials
Jennifer A. Ciezak, S. F. Trevino
Theoretical study of hydrogen-bonded complexes of bromophenols with ammonia: Correlations and predictions of pKa values
Jun Han, Fu-Ming Tao
Toward the development of an accurate virtual screening protocol: Recent improvements in protein ensemble docking
Luciano Mueller, Daniel L. Cheney
Computational analysis of the folding pathway of a mutant cold shock protein
Sergio Urahata, Adam Clarke, Alfredo E Cardenas
MM/PBSA studies on conformational changes of Yersinia Protein Tyrosine Phosphatase and use in structure-based inhibitor design
Xin Hu, C. Erec Stebbins
Molecular dynamics simulations of R67 DHFR: Investigation of the cooperative binding
Chuanyin Shi, Jennifer L. Radkiewicz
New Krypton bonded molecules: A theoretical study
Scott Yockel, Angela K. Wilson
Binary QSAR-based library design
Hua Gao
Revisiting the estimation of relative free energies from a single ensemble
Daniel J. Price, Charles L. Brooks III
RMSD: Routine measure stirs doubts
Jeremy J Yang
A novel MD/BD model for the simulation of multi-scale
Peter E Krouskop, Jeffry D. Madura
Active site structure and reaction mechanism of DNA polymerase β studied by molecular dynamics simulation and QM/MM method
Ping Lin, Lee G. Pedersen
Classical and ab initio molecular dynamics of quartz surfaces
Alexander D. MacKerell Jr., Pedro E. M. Lopes
Conformationally sampled pharmacophore for δ opioid ligands
Denzil Bernard, Andrew Coop, Alexander D. MacKerell Jr.
Controllable water channel gating of nanometer dimensions
Rongzheng Wan, J. Li, Hangjun Lu, Haiping Fang
Development and parametrization of MMFF/NQEq
Naofumi Nakayama, Shigeaki Obata, Hitoshi Goto
Development of fragment-based chemical descriptors using novel frequent common subgraph mining approach and their application in QSAR modeling
Raed Khashan, Weifan Zheng, Jun Huan, Wei Wang, Alexander Tropsha
Development and application of a novel software for asymmetric catalyst design
Christopher R. Corbeil, Nicolas Moitessier
Paper Withdrawn
Folding Trp-cage to atomic resolution: Searching parameter space for a free-energy minimum
Olgun Guvench, Charles L. Brooks III
Hydration and dewetting near graphite-CH3 and graphite-COOH plates
Jingyuan Li, Ting Liu, X. Li, Lei Ye, Huajun Chen, Haiping Fang, Zhaohui Wu, Ruhong Zhou
Inhibition of protein-protein interactions in the extracellular signal-regulated kinase (ERK)
Alba T. Macias, Chad N Hancock, Eun Kyoung Lee, Su Yeon Yu, Alexander D. MacKerell Jr., Paul Shapiro
Investigating the effects of methanol and n-octane entrainers on solubility and microscopic structure in supercritical carbon dioxide
Kelly E. Anderson, J. Ilja Siepmann
Learning chemistry from available compounds
Geoffrey Skillman, Roger Sayle
Library design based on privileged structures through docking and direct design in the protein binding pocket
Christof Gerlach, Hans FG Velec, Michael Smolinski, David G. Hangauer, Andreas Heine, Gerhard Klebe
Ligand refinement with combined force field and shape potential
Stanislaw Wlodek, Geoffrey Skillman, Anthony Nicholls
Mapping protein-ligand binding free energy contributions solely onto the ligand atoms
Sathesh Bhat, Enrico O. Purisima, Traian Sulea
Modeling of interfaces: Adsorption of 2-methyl-4-nitroaniline on hydrogen-terminated Si(100) 2x1 surface
Suely M. Black, Sheena Inge
Molecular docking and analysis of conformation adopted by tetrapeptide inhibitors into active site of thrombin
Cristina C. Clement, Manfred Philipp
Molecular dynamics of helical m-phenylene ethynylene foldamer with PEG side chains
One-Sun Lee, Jeffery G. Saven
Molecular modeling study of binding between DNA and CC-1065 analogue
Guangyu Sun, Marc C Nicklaus, Denise P. Simmons, Jing-Yu Lai
New estimate of beta-sheet folding cooperativity based on molecular dynamics simulations of a three-stranded beta-sheet
Daniel R. Roe, Viktor Hornak, Carlos Simmerling
Predictive tools for structure-based drug design: A comparative study of force field-based scoring functions
Pablo Englebienne, Nicolas Moitessier
Probing inherent helical preferences in Pt-beanpole complexes using molecular mechanics
Per Ola Norrby, John A. Gladysz, Fedor A. Zhuravlev
Schering-Plough 3-D: A web-based application to share 3-D project information
Johannes Voigt, Ravi Radhakrishnan, Corey Strickland
Standard reference simulations for docking and scoring: Enabling robust computational screening for drug design
A. Jayne Oliver-Kapur, Anne M. Chaka, Michael K. Gilson, Frederick P Schwarz
Stereoselectivity of hydroxyethyl azide reactions
Donna G. Withrow, Jennifer L. Poutsma
Studies on different interactions of beta-cyclodextrin with ferrocene derivatives and adamantane derivatives
Ming Ning, Richard E. Brown
Techniques for efficiently studying reactive events with electronic structure based biasing and transition path sampling
Christopher N. Rowley, Nicholas J. Mosey, Tom K. Woo
Theoretical study of the optical properties of Rhodamine 6G in Ag-ethanol suspension
AlTrev C. Sykes, Suely M. Black
Two mechanisms served by a single transition state: The branching ratio for CH2O•¯ + CH3Cl on improved potential energy surfaces
Jie Li, Xiaosong Li, Sason Shaik, H. Bernhard Schlegel
Unraveling the role of (6-4) Photolyase in DNA repair through homology modeling, consensus docking, and MD simulations
Chris Harrison, Olaf Wiest
Virtual screening of chemical libraries based on predictive QSAR methods
Mei Wang, Shuxing Zhang, Scott Oloff, Alexander Golbraikh, Harold Kohn, Alexander Tropsha
Visualization and interpretation of computational models
Kevin Schmidt, Brian Kelley, Joe Corkery, Jon Christopher, Robert Tolbert
Wavelet transforms for calculating time-dependent vibrational frequencies from dynamics simulations
Ralph A. Wheeler, Asif Rahaman
A simulation study of the binding modes of formamido-pyrimidine bound to DNA containing 8-oxo guanine
Kun Song, Arthur P. Grollman, Carlos de los Santos, Carlos Simmerling
Ab initio studies of a 1,2,3,5-tetrazocine
Sarah A Kebbell, Dermot F Brougham
Ab-initio calculations on the energetics of H2 oxidation by FeO+ using GGA+U
Heather J. Kulik, Damian Scherlis, Nicola Marzari
Accurate calculations of interaction energies of H-bonded clusters
Jun Cui, Valerie N. McCarthy, Richard A. Christie, Kenneth D. Jordan
AEI: Exploring solvent effects and mechanisms for organic reactions using computational methods
Orlando Acevedo, William L. Jorgensen
Atomic-scale mechanism of met repressor function
Jieru Zheng, Ilya Balabin, David N. Beratan
Calculation of absorption line shape based on reduced density matrix approach
Mino Yang
CHARMM Drude polarizable force field parameter development for model compounds representative of biological systems
Igor V. Vorobyov, Victor M. Anisimov, Alexander D. MacKerell Jr.
Collaborative filtering on a family of biological targets
Dumitru Erhan, Pierre-Jean L'Heureux, Yoshua Bengio, Shi Yi Yue
Comparison of methods of density functional theory modeling of the specific rotation of amino acid solutions
Matthew D. Kundrat, Jochen Autschbach
Comparisons of potential energy landscapes and conformations of polyalanine with different force fields by new molecular dynamics simulation protocols
Zunnan Huang, Ralph A. Wheeler
Computation of quartic potential energy surfaces and excited vibrational levels of H2O
Nicole R. Brinkmann, John L. Davisson, Michael H. Cortez, William F. Polik
Computational analysis and prediction of bioisosteres
Joseph Ban, Robert Tolbert, Anthony Nicholls, Geoffrey Skillman
Computational study on the vanadium-catalyzed asymmetric oxidation of sulfides
David Balcells, Feliu Maseras, Gregori Ujaque
Cycloreversion of the (6-4) photolesion: DFT studies of the DNA repair mechanism
Chris Harrison, Olaf Wiest
Digging the past for a clue: A novel in-silico approach for new leads on 4-OH-pyran-2-ones HIV protease inhibitors
Barun Bhhatarai, Rajni Garg
Dissociation energy estimation of insulins using all-electron density functional calculation
Toru Inaba, Fumitoshi Sato
Do similar ligands bind in a similar fashion?
Jonas Boström, Anders Hogner, Stefan Schmitt
Drying and hydrophobic collapse in the multi-domain protein and protein oligomers
Xuhui Huang, Ruhong Zhou, Pu Liu, Claudio J. Margulis, BJ. Berne
Dynamic equilibrium between fast and slow forms of thrombin: A structural investigation of thrombin paradox
Divi Venkateswarlu, Lee G. Pedersen
Effect of solvent on the stereoselectivity of reactions between hydroxyalkyl azides and ketones
Anna K. Manukyan, Jennifer Radkiewicz-Poutsma
Exhaustive computational analysis of peptides for the fragmentation in low-energy dissociation mass spectrometry
Kazuhiko Fukui, Yutaka Akiyama
Forward-backward semiclassical dynamics
Nicholas J Wright, Nancy Makri
Homology modeling, docking and molecular dynamics simulation of class I HDACs
Di-Fei Wang, Olaf G. Wiest, Paul Helquist
Impact of multiple conformations on fingerprint descriptors uses in QSAR
Pierre-Jean L'Heureux, Benoit Cromp, Shi Yi Yue, Yoshua Bengio
Paper Withdrawn
Modeling gene regulatory networks
Peng Zhang, Ming Ouyang, William J. Welsh
Molecular dynamics simulations of a DNA strand containing two thymine dimers
Lauren L O'Neil, Olaf Wiest
Monte Carlo simulation study for QSPR of solvent effect on the selectivity of 18-Crown-6 between Gd3+ and Yb+3 ions
Hag Sung Kim
Origins of the high affinity binding of the biotin-(strept)avidin complex
Jason DeChancie, K. N. Houk
Reduction of computational requirements and trends for high accuracy description of molecular properties
Benjamin Mintz, Angela K. Wilson
Simulation of water soluble potassium channel
One-Sun Lee, Jonathan Bronson, Jeffery G. Saven
Solvent effect on relative Gibbs free energy and structural property of Eu3+ to Yb3+ ion mutation: A Monte Carlo simulation study
Hag Sung Kim
Structural and thermodynamic properties of ammonium chloride clusters
Robert Q. Topper
Study on fiber bonding strength in modeling of paper tensile strength with fiber characteristics
J. S. Tao, D. B. Yan, H. B. Liu, Y. G. Xu, S. L. Kou, H. k. Ge
Computational prediction of adenosine receptor homodimerization
Soo-Kyung Kim, Kenneth A. Jacobson
New tool for the interrogation of macromolecular structure
Francisco Torrens

Symposium Grid -- Division of Computers in Chemistry -- Session Listing

The 230th ACS National Meeting, in Washington, DC, Aug 28-Sept 1, 2005