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· COMP Symposium Grid · COMP Session Listing |
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| COMP | Tuesday, March 15, 2005 | ||
Poster | |||
Poster Session | |||
| Organizer: | Wendy D. Cornell | ||
| 137 | Gaussian-weighted RMSD superposition of proteins Kelly L. Damm, Heather A. Carlson | ||
| 138 | Binding MOAD (Mother of All Databases) Mark L. Benson, Liegi Hu, Richard D. Smith, Michael G. Lerner, Heather A. Carlson | ||
| 139 | Database mining to characterize protein-ligand binding sites Richard D. Smith, Nickolay Khazanov, Heather A Carlson | ||
| 140 | Creating a smart virtual screening workflow: Application of E. coli DHFR primary HTS data Shikha Varma, Luke S. Fisher, Teresa A. Lyons, Deqi Chen | ||
| 141 | Omega2: Conformer generation redux Matthew Stahl, Geoffrey Skillman | ||
| 142 | SAESAR: Shape and electrostatics in structure activity relationships Norah E. MacCuish, Anthony Nicholls, John D. MacCuish | ||
| 143 | Efficient charges: Optimal ligand charges for binding that might actually work Anthony Nicholls, Sharangdhar Phatak, Glen E. Kellogg | ||
| 144 | Shape and electrostatic similarity across a large-scale database of vendor-available compounds Robert Tolbert, Anthony Nicholls, Geoff Skillman, Mike Tennant | ||
| 145 | Structure-based design, molecular modeling and biophysical studies of conformation adopted by tetrapeptides with inhibitory activity for thrombin Cristina Clement, Janet Gonzalez, Rafael Alcantara, Manfred Philipp | ||
| 146 | Rapid evaluation of compound oral bioavailability using in vitro and in silico ADME properties S. Frank Yan, Kaisheng Chen, Lana Schaffer, Min Wu, Yingyao Zhou | ||
| 147 | Role of quantitative structure activity relationship (QSAR) in understanding HIV-1 binding domain and designing protease inhibitors Barun Bhhatarai, Rajni Garg | ||
| 148 | Three for three: De novo design of multiple novel chemotypes of T-type calcium channel blockers Daniel L. Cheney, Jon J. Hangeland, Todd J. Friends, Paul C. Levesque | ||
| 149 | Towards the solution structure of a “mini-insulin” Julien Pecher, Guillaume Le Flem, Patrick Bogdanowicz, Jean-Pierre Pujol, David A. Case, Jacques Rochette, Francois-Yves Dupradeau | ||
| 150 | Towards validation of a model to identify hERG potassium channel blockers Laura C. Van Zant, A. Michiel van Rhee, Neil A. Castle, Christopher P. Silvia | ||
| 151 | A complete model of human type I collagen monomer Ivan Vinogradov, Darren J. Anderson, M. Cynthia Goh | ||
| 152 | Ab initio protein loop prediction in internal coordinate space Jianghong An, Maxim Totrov, Ruben Abagyan | ||
| 153 | Characterization of drug and drug carrier interactions by using computational chemistry and X-ray crystallography Lingyun Xiao, Ronald R. Burnette, Ilia A. Guzei | ||
| 154 | Comparative analysis of putative agonist binding modes in the human A1 adenosine receptor Hugo Gutiérrez de Terán, Johan Åqvist, Ferran Sanz | ||
| 155 | Comparative QSAR as a cheminformatics tool in the design of HIV-1 protease inhibitors Rajni Garg, Barun Bhhatarai | ||
| 156 | De novo structure-based design of ion receptors Benjamin P. Hay, Alexander A. Oliferenko | ||
| 157 | DNA and estrogen receptor interaction revealed by the fragment molecular orbital calculation Toshio Watanabe, Yuichi Inadomi, Shigenori Tanaka, Kaori Fukuzawa, Tatsuya Nakano, Lennart Nilsson, Umpei Nagashima | ||
| 158 | Hierarchical QSAR (HiQSAR) approach to predicting dermal penetration Brian D. Gute, James Riviere, Ronald E. Baynes, Subhash C. Basak | ||
| 159 | Low-resolution modeling of the ribosome assembly of the 30S subunit by molecular dynamics simulations Qizhi Cui, David A. Case | ||
| 160 | Modeling and predicting the structure of G-protein-coupled receptors Mayako Michino, Wonpil Im, Jianhan Chen, Charles L. Brooks III | ||
| 161 | Modeling human K+ channel and exploring ligand binding using molecular dynamics Fredrik Österberg, Johan Åqvist | ||
| 162 | Modeling peptide association in amyloid-forming peptides Ronald D. Hills Jr., Charles L. Brooks III | ||
| 163 | Modulation of steric forces in the minor groove of DNA Sarah A. Mueller-Stein, Anne Loccisano, Steven M. Firestine, Jeffrey D. Evanseck | ||
| 164 | Molecular dynamics simulations of a RNA-morpholino hybrid Edmond Y. Lau, Michael E. Colvin | ||
| 165 | Molecular dynamics simulations of human tRNALys,3UUU anticodon stem-loop: Determination of the role of nonstandard bases Nina E. McCrate, Mychel E. Varner, Katie L. Schembri, Amanda E. Combs, Maria C. Nagan | ||
| 166 | Predictor@home: A multiscale, distributed approach for protein structure prediction Chahm An, Michela Taufer, Charles L. Brooks III | ||
| 167 | Accurate prediction of binding sites for diverse protein targets using fragment-based grand canonical Monte Carlo Simulations Suo-Bao Rong, Ted Fujimoto, Jennifer Ludington, Brian Alger, Igor Shkurko, Matthew Clark, Jeffery S. S. Wiseman, Frank P. Hollinger | ||
| 168 | Incorporating protein flexibility into drug design: HIV-1 protease as a test case Kristin L. Meagher, Michael G. Lerner, Heather A. Carlson | ||
| 169 | Protein ensemble docking: Comparison of fixed charge and polarizable forcefields in scoring Luciano Mueller, Daniel L. Cheney | ||
| 170 | Strategies for efficient ligand-receptor docking: Typical case studies Akbar Nayeem, Stanley Krystek Jr. | ||
| 171 | Virtual screening approach: Application of a hydropathic forcefield to 3D database searches Micaela Fornabaio, Fraydoon Rastinejad, Shilpa Kharalkar, Martin Safo, Donald J. Abraham, Glen E. Kellogg | ||
| 172 | Docking studies and ligand recognition in folypolyglutamate synthetase Xiao-Jian Tan, Heather A. Carlson | ||
| 173 | Docking to large ensembles of homology models reliably explains the substrate binding differences in Cytochrome P450 1As of human and fish species Jahnavi C. Prasad, Carlos J. Camacho, John J. Stegeman, Sandor Vajda | ||
| 174 | Computational prediction of structure, substrate binding mode, mechanism and rate for a malaria protease with a novel type of active site Sinisa Bjelic, Johan Åqvist | ||
| 175 | A structure-based approach to Akt/PKB inhibition Dawoon Jung, Martino Forino, Maurizio Pellecchia | ||
| 176 | Docking of phthalate monoesters to PPAR-ã Taner Kaya, Scott C. Mohr, David J. Waxman, Sandor Vajda | ||
| 177 | Quantitative structure–activity relationship analysis of pyridinone HIV-1 reverse transcriptase inhibitors using the k nearest neighbor method and QSAR-based database mining Jose Luis Medina-Franco, Alexander Golbraikh, Rafael Castillo, Alexander Tropsha | ||
| 178 | QSAR study of hemostatic labdane diterpenoids M. A. Turabekova, U. N. Zainutdinov, Sh. I. Salikhov | ||
| 179 | 2-Pyrimidinethiol and methyl-2-pyrimidinethiols: A computational study of tautomers and dimers Fillmore Freeman, Henry N. Po | ||
| 180 | A crystal force field: Evaluation of short-range intermolecular interactions for representation of X-ray crystal structures in Cambridge Structure Database Hitoshi Goto, Shigeo Obata, Naofumi Nakayama | ||
| 181 | A theoretical study of active site proton swapping in Subtilisin Carlsberg during catalysis Marc D. Legault | ||
| 182 | A theoretical study of the enantioselectivity of Rhizomucor Miehei lipase during catalysis Brenda De Leon Rivera, Marc D. Legault, Gabriel L. Barletta | ||
| 183 | A theoretical study on fragmentation pathways and mechanisms of protonated β-alanine Man Kit, Jackie Cheng, On Ying, Onyx Chan, S. Abirami, N. L. Ma, C. W. Tsang | ||
| 184 | Ab initio genetic algorithm based elucidation of multiply aromatic clusters Anastassia N. Alexandrova, Alexander I. Boldyrev, Hua-Jin Zhai, Lai-Sheng Wang | ||
| 185 | Absolute and relative entropies from computer simulation with applications to ligand binding Jens Carlsson, Johan Åqvist | ||
| 186 | Accurate predictions of protein-protein binding free energies Martin Almlöf, Bjørn Brandsdal, Johan Åqvist | ||
| 187 | Automatic clustering of probe molecules to define surface complementarity: Applications to protein-protein interfaces Michael G. Lerner, Heather A. Carlson | ||
| 188 | Binding affinity studies of Plasmepsins from Plasmodium falciparum Martin Nervall, Johan Åqvist | ||
| 189 | Binding energy calculation for theophylline-RNA aptamer with generalized BAR method Yoshiaki Tanida, Masakatsu Ito, Hideaki Fujitani, Michael R. Shirts, Christopher D. Snow, Guha Jayachandran, Vijay S. Pande | ||
| 190 | Comparison of arbitrary versus tailored similarity spaces in property estimation Brian D. Gute, Subhash C. Basak, Denise Mills, Douglas M. Hawkins | ||
| 191 | Computation of the absorption spectrum of green fluorescent protein Steven Trohalaki, Soumya S. Patnaik, Ruth Pachter | ||
| 192 | Computational approaches to MEK1 and MEK2 structure determination and inhibitor design Huifen Chen, Jeffrey F. Ohren, Christopher E. Whitehead, Alexander Pavlovsky, Erli Zhang, Peter Kuffa, Chunhong Yan, Patrick McConnell, Amy Delaney, David T. Dudley, Charles Hasemann | ||
| 193 | Computational investigation of structural and electronic characteristics of a series of glycosidase inhibitors and their relationship to experimental activity data Robert D. Anderson, M. C. Milletti | ||
| 194 | Computational modeling study of the C-terminal RING-finger domain of HDM2 Zengjian Hu, Tangayi Githu, Donnell Bowen, William M. Southerland | ||
| 195 | Computational studies of the potential inhibitors of the copper-containing enzyme lysyl oxidase Faina Ryvkin, Marina Dang | ||
| 196 | Computational studies of the structure and bonding of sulfur and phosphorous ylides Jean M. Standard, Beth A. Copack, Rebecca J. Steidl | ||
| 197 | Conformational interconversion of alanine dipeptide from 100 nanosecond molecular dynamics simulations by implicit and explicit solvation methods Ryan A. Newton, Jeffrey D. Evanseck | ||
| 198 | Conformational isomerization kinetics of a dipeptide, N-acetyl - tryptophan methyl amide (NATMA): A non-RRKM approach Johnson K Agbo, David M. Leitner | ||
| 199 | Conformational study of small molecules in crystallographically determined structures Rajeshri G. Karki, Marc C Nicklaus | ||
| 200 | Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DiSCO) algorithm Qing Zhang, Daniel A. Beard, Tamar Schlick | ||
| 201 | Potential ligand design for Dengue virus using high throughput screening, binding affinity evaluation and pharmacophore/scaffold identification Zhigang Zhou, Carol Post | ||
| 202 | Design and conformational analysis of paclitaxel derivatives of nitroimidazole Iwona Weidlich, S. Sobiak | ||
| 203 | Development of a special purpose parallel computer for the first principles DVXƒ¿ calculations Umpei Nagashima, Tohru Sasaki | ||
| 204 | Docking studies and 3D-QSAR analysis for inducible nitric oxide synthase inhibitors Yoko Kyoya, Shigeo Ueda, Akihiro Yano, Yukio Tominaga, Motoharu Ido, Motoji Kawasaki, Iwao Fujiwara | ||
| 205 | Effect of glycosylation on a model peptide Sarah M Tschampel, Robert J. Woods | ||
| 206 | Efficient linear-scaling Ewald method for combined QM/MM calculations: Development and comparison with stochastic boundary and spherical cut-off methods Kwangho Nam, Jiali Gao, Darrin M. York | ||
| 207 | First-principles calculation of the binding free-energy landscape of a trypsin-ligand complex Olgun Guvench, Charles L. Brooks III | ||
| 208 | Forcefield parameterization of inhalational anesthetics, halothane and isoflurane: An ab initio study Satyavani Vemparala, Ivaylo Ivanov, Michael L. Klein | ||
| 209 | Fuzzy relational clustering of molecular conformations using novel features based on DNA base-pair step parameters Milind Misra, Deepa Pai, Rohan Woodley, Amit Banerjee, Rajesh N. Davé, Liang-Yu Shih, Xiang-Jun Lu, A. R. Srinivasan, Wilma K Olson, Carol A. Venanzi | ||
| 210 | How does autophosphorylation modulate catalysis function and regulation in cAMP-dependent protein kinase? Yuhui Cheng | ||
| 211 | Investigating targets of antibacterial cysteine protease inhibitors Leslie A. Vogt, Jeffrey P. Wolbach | ||
| 212 | Kinetic and geometrical isotope effects in hydrogen-atom transfer reaction: Application of multi-component MO method Takayoshi Ishimoto, Masanori Tachikawa, Umpei Nagashima | ||
| 213 | Modeling of triclosan analogs for enoyl reductase inhibition Jonilyn G. Longenecker, Paul D. Schettler Jr., Richard R. Hark, Jeffrey P. Wolbach | ||
| 214 | Molecular simulations of model Langmuir monolayers Leslie V. Villalobos-Rivera, Gustavo E. López | ||
| 215 | Nitrosation of melatonin Jamie M. Rintelman, Mark S. Gordon, Julia E. Rice | ||
| 216 | On the convergence of a hybrid parallel tempering Tsallis statistics Monte Carlo algorithm Hanbin Liu, Kenneth D. Jordan | ||
| 217 | Pharmacophore identification and antidiabetic activity prediction in the class of guanidino- and aminoguanidinoacetic acid compounds Aleksandr V. Marenich, Isaac B. Bersuker, James E. Boggs | ||
| 218 | Q: A novel method to simulate the solvation of hydrophobic surfaces by water and its application to the estimation of protein-ligand binding constants Arthur M. Doweyko, Stephen R Johnson | ||
| 219 | Rare gases inserted into biological building blocks: A theoretical study of glycine - Rg compounds (Rg=Xe, Kr, Ar) Galina M. Chaban | ||
| 220 | Rate constant calculation of ligand binding with solvation force determined by boundary elementary method Ben Zhuo Lu, David Zhang, Andrew J. McCammon | ||
| 221 | Sila-Pummerer rearrangement of cyclic sulfoxides: A computational study of sulfonium ylide intermediates Fillmore Freeman, Svetlana V. Kirpichenko, Bagrat A. Shainyan | ||
| 222 | Similarity-based chemical clustering techniques Brian D. Gute, Subhash C. Basak, Denise Mills | ||
| 223 | Tautomerization of the HBO base pair model in the DNA major and minor grooves Francois-Yves Dupradeau, Chengzhi Yu, Ralph Jimenez, Floyd E. Romesberg, David A. Case | ||
| 224 | Theoretical study on glucose polysaccharides Jen-Shiang K. Yu | ||
| 225 | Unbinding study of edema factor-calmodulin complex using steered molecular dynamics Kristine A Baker, Jeffrey D. Evanseck, Steven M. Firestine | ||
| 226 | Unintended consequences of periodic boundary conditions: Particles of different mass have different effective temperatures Randall B. Shirts, Scott R. Burt, Aaron M. Johnson | ||
| 227 | Predicting chemical shielding in proteins: A QM/MM study combined with MD simulations Seongho Moon, David A. Case | ||
| 228 | Understanding C2-substituent effects of bis(oxazoline) copper(II) catalyzed Diels-Alder reactions by density functional computation Edward G. Franklin, Jason DeChancie, Jeffrey D. Evanseck | ||
| 229 | Understanding the proficiency of OMP Decarboxylase: An ab initio study Courtney L Stanton, K. N. Houk | ||
| 230 | A computational study of the competing pathways of rearrangement, HF and HCl elimination reactions of CF3CF2CH2Cl and CF3CHClCF3 William C. Everett, Bert E. Holmes, George L Heard | ||
| 231 | A QM/QM’ approach to modeling the Zn(II)/Cu(I) core of a protein Melinda A. Harrison, Llaria Ciofini, Jeffrey D. Evanseck, Carlo Adamo, Charles T. Dameron | ||
| 232 | Ab-initio fragment orbital theory: Application to the excited states of some organometallic compounds Guru P Das, Jean-Philipe Blaudeau | ||
| 233 | Application of variational reduced-density-matrix theory to organic molecules Gergely Gidofalvi, David A Mazziotti | ||
| 234 | Bonding or antibonding, an overlap population study Xin Liu, Changgong Meng, Changhou Liu | ||
| 235 | Calculating low energy reaction pathways in proteins and RNA: A QM/MM implementation of the Nudged Elastic Band (NEB) method Ross C Walker, David H. Mathews, David Case | ||
| 236 | Computational studies of the phosphorylation reaction in protein kinase A: Ab-initio QM/MM approach Marat Valiev, John H. Weare | ||
| 237 | Computational study of epoxide ring-opening reactions of 2,3-anhydrosugars Peng Tao, Raghavan B. Sunoj, Matthew P. DeMatteo, Todd L. Lowary, Christopher M. Hadad | ||
| 238 | Computational study of the reaction mechanism of ethylenimine with DNA Patricia M. Todebush | ||
| 239 | Computational study of twisted intramolecular charge transfer (TICT) characteristics of substituted pyrrolyl pyridines Jessica L. Menke, Eric V. Patterson | ||
| 240 | Determination of the conformation of 2-hydroxy, 2-amino and 2-fluoro benzoic acid dimers in CDCl3 using 13C NMR and DFT/NBO analysis: The central importance of the carboxylic acid carbon Ronald R. Burnette, Frank Weinhold | ||
| 241 | DFT and ONIOM studies on the oxalate oxidase (Oxo) catalytic mechanism Tomasz Borowski, Arianna Bassan, Nigel G.J. Richards, Per Siegbahn | ||
| 242 | Energetics and barriers of pericyclic reactions involving alkene analogues R2BPR'2 and R2AlNR'2 Thomas M. Gilbert, John M. Bailey | ||
| 243 | Large-scale molecular orbitals based on fragment molecular orbital method solved by projection method Yuichi Inadomi, Hiroaki Umeda, Toshio Watanabe, Tetsuya Sakurai, Umpei Nagashima | ||
| 244 | ONIOM computations of the water dimer structure and thermodynamics Stephen Arnstein, Jeffrey D. Evanseck | ||
| 245 | Parallel Fock matrix construction on layered multi-processor system Hiroaki Umeda, Yuichi Inadomi, Hiroaki Honda, Umpei Nagashima | ||
| 246 | Modeling MAO (methylaluminoxane) formation Lacramioara Negureanu, Randall W. Hall, Les G. Butler | ||
Symposium Grid -- Division of Computers in Chemistry -- Session Listing