COMPTuesday, August 18, 2009

6:00 PM-8:00 PM Walter E. Washington Convention Center -- Ballroom A, Poster
Poster Session
Organizer:Emilio Xavier Esposito
Sequence effects on the charge transfer in DNA
Alexander Balaeff, Shahar Keinan, Ravindra Venkatramani, David N. Beratan
3D-QSAR of cell-based biological activities: Integration of disposition function with multispecies, multimode CoMFA
Senthil Natesan, Stefan Balaz
Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins
Vagmita Pabuwal, Zhijun Li
Designing specific or promiscuous drug molecules: Theory, methods development, and application to the HIV-1 system
Mala L Radhakrishnan
Modeling the sorption dynamics of aluminum hydride using a reactive force field
Julius GO. Ojwang, Adri CT. van Duin, William A Goddard III, Gert Jan Kramer, Rutger A. van Santen
pH-Dependent conformational states of AcrA protein: Implications for the assembly of AcrAB-TolC multidrug efflux pump
Jason Wallace
Preferences across phases: Structural preferences in Group 2 dihalide and dihydride monomers, dimers, trimers, and solids
Kelling J. Donald
3D-QSAR model for inhibition requirements for hASBT using glutamyl-chenodeoxycholate (glu-CDCA) conjugates of aniline
Chayan Acharya, Rana Rais, James E. Polli, Alexander D. MacKerell Jr.
A Kirkwood-Buff force field for thiols, sulfides, and disulfides
Nikolaos Bentenitis, Paul E. Smith
A tight-binding study of ionic hydrogen-bond networks in ion solvation
Yi-Lei Zhao, Carlos A. Gonzalez, M. Meot-Ner
Ab initio studies of ether-carbene ylides
Jean M. Standard, Ryan D. Quinn
Accelerating DFT calculations with GPU: A hybrid computing approach
Jing Kong, Zhengting Gan, Yihan Shao, Roberto Olivares-Amaya, Alán Aspuru-Guzik
Adaptively biased dynamics study of the excited states of TIM
Sishi Tang, David Case
A docking model for convulxin and convulxin-like proteins with human glycoprotein VI
Yufeng J. Tseng, Cheng-chieh Tsai
Modeling macromolecular structure, dynamics, and energetics
Jennifer L. Knight, Charles L. Brooks III
Solving problems of biomedical relevance through multiscale computational methods and high performance computing
Karunesh Arora, Charles L. Brooks III
Algorithmic improvements in DOCK6 for enhanced conformational sampling
Sudipto Mukherjee, Trent E. Balius, Robert C. Rizzo
Paper Withdrawn
Large-scale QM/MM calculations of protein-ligand interaction in Thrombin S1 pocket
Marek Freindorf, Jing Kong, Bernhard Baum, Menshawy Mohamed, Mohamed Zayed, Gerhard Klebe, David G. Hangauer
Support vector machine classification model of Pubchem hERG bioassay data with 4D-fingerprint and MOE descriptors
Yufeng J. Tseng, Meng-yu Shen, Bo-Han Su
In silico binary QSAR model based on 4D-fingerprints and MOE descriptors for hERG blockage evaluation
Yufeng J. Tseng, Bo-Han Su, Meng-yu Shen
2D- and 3D-Similarity based classification systems for substrate prediction of ABCB1
Rita Schwaha, Gerhard F. Ecker
Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions
Allyn Brice, Brian N. Dominy
Annelated derivatives of cyclooctatetrane in which σ→π* electron transfer is energetically favorable
Xin Zhou, David A. Hrovat, Weston Thatcher Borden
Application of flexible volumetric alignment in ligand based virtual screening
Adrián Kalászi, Gábor Imre, Ödön Farkas, Miklos Vargyas, Ferenc Csizmadia
Automatic and systematic search for routes of chemical reactions in large flexible systems with a given reaction center by the microiteration technique and the GRRM method
Satoshi Maeda, Koichi Ohno, Keiji Morokuma
Biophysical resolution: How tolerant are binding free energy calculations to errors in protein structure?
Manoj Singh, Brian N. Dominy
Calculations of the relative energies of the low-lying electronic states of 2-methylenedihydrophenalene-1,3-diyl: Effects of a 1,8-naphtho bridging group on trimethylenemethane and of a vinylidene bridging group on 1,8-naphthoquinodimethane
Hao Dong, David A. Hrovat, Helmut Quast, Weston Thatcher Borden
CHARMM additive all-atom force field for aldopentofuranoside carbohydrates and fructofuranoside
Elizabeth R Hatcher, Olgun Guvench, Alexander D. MacKerell Jr.
Comparison of biomolecular force fields for the peptide group and ionic sidechains
Myungshim Kang, Paul E. Smith
Computational analysis of crystal shapes as modified by surrounding microstructure and effect on crystal size distribution
Roddy V. Amenta
Computational analysis of HIVgp41 mutants in complex with peptide based fusion inhibitors
Brian Edward McGillick, Trent E. Balius, Sudipto Mukherjee, Robert C. Rizzo
Computational approaches to understand the interaction of HIV-1 integrase and its inhibitors from natural sources
Zengjian Hu, Dagang Chen, Lanxiang Dong, Xuhong Wang, William M. Southerland
Computational studies on carboxyphosphate
Kyle W. Reeping, Sai Pakkala, Steven M. Firestine, Jeffrey D. Evanseck
Computational study of intramolecular hydrogen bonding in arylamide compounds: Delocalization effect
Dana Marie Todd, Jhenny Galan, Zhiwei Liu, Guillermo Moyna, Vojislava Pophristic
Computational study of the conformational properties of the amino acid side chains
Xiao Zhu, Alexander D. MacKerell Jr.
Continuum electrostatic and free energy perturbation calculations on leucine transporter complexed with tricyclic antidepressants
Kalyan Immadisetty, Jonathon D. Gibbons, Jeffry D. Madura
Correlation between quantum mechanical/molecular mechanical (QM/MM) docking performance and binding site classification
Jae Yoon Chung, Jung-Mi Hah, Art E. Cho
Coupling accelerated molecular dynamics methods with thermodynamic integration simulations
Cesar Augusto F. de Oliveira, Donald Hamelberg, J Andrew McCammon
Density functional theoretical study on redox-dependent hydrogen bonding between amide and arylurea
Young Seuk Cho, Hyun Cho, Han Young Woo, Jong-Man Kim, Sungu Hwang
Density functional theoretical study on the pKa values of bipyridines
Sungu Hwang, Sang Woo Joo, Yun Hee Jang
Development of serotonin and norepinephrine transporter inhibitor pharmacophore models: Design of selective ligands
Elizabeth M. Collantes, Daniel F. Ortwine
DFT calculations on the stability of 2D covalent organic frameworks
Daejin Kim, Dong Hyun Jung, Kyung-Hyun Kim, Areum Lee, Jaheon Kim, Kihang Choi, Seung-Hoon Choi
DFT study of the effect of Al2O3 support on Pt catalytic activity
Jennifer Synowczynski, Jan Andzelm, Dionisios G. Vlachos
Docking simulation on the inhibitor of exo-polygalacturonase
Yong-Jae Lee, Eun-Hee Kim, Sungu Hwang
Dynamics of nitrous oxide in lipid bilayers at different hydrations: A molecular dynamics study
Eric Pinnick, Shyamsunder Erramilli, Feng Wang
Effect of the nucleotide modification on the conformation and stability of the triple DNA formation
Eva Darian, Andrey Semenyuk, Michael M Seidman, Alexander D. MacKerell Jr.
Elucidation of binding profile similarities across structurally diverse ligands using a 3D dopamine transporter model
Sankar Manepalli, Jeffry D. Madura, David J. Lapinsky, Christopher K. Surratt
Enzymatic DNA base flipping mechanism examined via nudged elastic band simulations
Christina Bergonzo, Arthur J. Campbell, Carlos De los Santos, Arthur P. Grollman, Carlos Simmerling
Implementation of a novel coarse-grain model using rhodopsin in a lipid bilayer
Kenny Nguyen, Jhenny Galan, Zhiwei Liu, Preston Moore
Intrinsic Lewis base strength based upon valency
Joseph J Rosmus, Joshua A Plumley, Jeffrey D. Evanseck
Key role of computational CNS penetration studies in selecting and advancing compounds in P2X7 analgesia project
Sanjay Srivastava, Marie Roumi, Rosemarie Panetta, Annie-Kim Gilbert, Simon J. Teague
Ligand-supported homology modeling of the human melanin concentrating hormone receptor 1 (MCH-R1)
Mohamed Helal, MItchell A. Avery
Mechanism of anesthetic binding to lipid bilayer
Nicolas Chen, Thuy Hien T. Nguyen, Julian Snow, Preston B Moore
Modeling of pillared covalent organic frameworks as the hydrogen storage material
Daejin Kim, Dong Hyun Jung, Kyung-Hyun Kim, Areum Lee, Jaheon Kim, Kihang Choi, Seung-Hoon Choi
Models for the nucleation and growth of calcium carbonate
John H Harding, Colin L Freeman, Mingjun Yang, David J. Cooke, James A. Elliott, Dorothy M Duffy, Jennifer Lardge, David Quigley, P. M. Rodger
Molecular dynamics of proteins embedded in a lipid bilayer
Thuy Hien Nguyen, Preston B Moore
Molecular dynamics of second-shell interactions in zinc finger binding sites
Megan L. Peach, Marc C. Nicklaus
Molecular dynamics simulations of complex mixed lipid bilayers to model yeast membranes
Joseph B. Lim, Jeffery B. Klauda
Molecular dynamics simulations of the quick micelle formation of Azotab in D2O solution: Micellar structure and the swing of two benzene rings
Chih-Ying Lin, Katherine Shing, C. Ted Lee
Molecular modeling of interaction between sAnk157-122 and obscurin6322-6339 in striated muscle
Taiji Oashi, Ben Busby, Chris D. Willis, Robert J. Bloch, Alexander D. MacKerell Jr.
Navigating molecular worms inside chemical labyrinths
Maciej Haranczyk, James A. Sethian
Novel protocols for modeling flexible loops: Implications for drug design
Karen A. Rossi, Carolyn A. Weigelt, Akbar Nayeem, Stanley R. Krystek Jr.
Numerical integration of the coupled rate differentials via a discretized Adomian decomposition
Jarod M Younker, Michael T Green
On the applicability of homology models of G protein-coupled receptors to computer-aided drug discovery
Santiago Vilar, Giulio Ferino, Stefano Costanzi
Optimal design of paper mill process energy with mathematical programming and three-link modeling
JS. Tao Sr., JG. Li Sr., HB. Liu
Parameterization of desipramine, imipramine, and clomipramine
Jonathon D. Gibbons, Jeffry D. Madura
Potential of mean force calculations of the free energy of binding of Type I antifreeze proteins at water/ice interface
A. Wierzbicki, Keith Battle, Jeffry D. Madura
Prediction of fold resistance for inhibitors of EGFR using all-atom molecular dynamics simulations
Trent E. Balius, Robert C. Rizzo
Probing protein-ligand interactions by ab initio NMR chemical shift calculations
Bing Wang, Xiao He, Kenneth M. Merz Jr.
Properties of alcohol water mixtures by computer simulation
Yuanfang Jiao, Feng Chen, Paul E. Smith
QSAR modeling and knowledge discovery of a large unbalanced dataset of hERG K+ channel blockers and openers
Kun Wang, Alexander Golbraikh, Bryan L. Roth, Alexander Tropsha
Quantitative conformationally sampled pharmacophore for μ opioid ligands
Ji Hyun Shim, Andrew Coop, Alexander D. MacKerell Jr.
Representation, searching, and enumeration of Markush structures: From molecules toward patents
Szabolcs Csepregi, Nóra Máté, Robert Wagner, T Csizmazia, Szilárd Dóránt, E Biro, Ferenc Csizmadia
Search for inhibitors of S100B-p53 interaction
E. Prabhu Raman, Shijun Zhong, Paul T. Wilder, Thomas H. Charpentier, David J. Weber, Alexander D. MacKerell Jr.
Simulation study of interprotein electron transfer in hemoglobin tetramers
Ravindra Venkatramani, Shahar Keinan, David N. Beratan
Structure-based drug design against pandemic influenza using all-atom molecular dynamics and docking
Rashi Goyal, Robert C. Rizzo
Surface tension, contact angle, and line tension in a liquid nanodroplet
D. Vladimir Perez, Chi-cheng Chiu, Steven O. Nielsen, Preston Moore
Targeted design of dual kinase inhibitors for breast cancer
Yulin Huang, Robert C. Rizzo
The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning
Tatsuya Yoshikawa, Kazuhiko Fukui
The effects of conformational variations on the packing of cup shaped molecules
Michael Roumanos, Miklos Kertesz, K. Travis Holman
The energetics of stop codon recognition on the ribosome
Johan Sund, Martin Andér, Johan Ĺqvist
The nature of intermolecular interactions in water-methanol complexes
Venkata S Pakkala, Joshua A Plumley, Jeffrey Evanseck
The role of human skin emanation in understanding how a mosquito repellent works
Jie Song, Zongde Wang, JInzhu Chen, Tingxin Yi, Guorong Fan, Shangxin Chen
Theoretical studies for the crystal structure prediction: Tests on indenopyrazine
Kyung-Hyun Kim, Daejin Kim, Areum Lee, Seung-Hoon Choi, Young-Il Park, Soo-Kang Kim, Chang-Hun Seok, Jong-Wook Park, Ji-Hoon Lee, Dong Hyun Jung
Training pKa and logP prediction
Jozsef Szegezdi, Ferenc Csizmadia
Vibrational and spin properties of radicals derived from ubiquinol (dihyroubiquinone)
Ralph A. Wheeler, Scott E. Boesch
Web services to promote GPCRs peptide mimetics
Wataru Nemoto, Kazuhiko Fukui, Hiroyuki Toh

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

The 238th ACS National Meeting, Washington, DC, August 16-20, 2009