Section A
Georgia World Congress Center -- B304
8:40 — Introductory Remarks. Weitao Yang.
8:50 —1. Van der Waals theory in the spirit of Maxwell. W. Kohn
9:20 —2. Van der Waals interactions from the exchange hole dipole moment. A. D. Becke, E. R. Johnson
9:50 —3. Applications of van der Waals density functional (vdW-DF). D. C. Langreth
10:20 — Intermission.
10:30 —4. Improvements in density functionals theory and applications to nanoelectronics. W. A. Goddard III
11:00 —5. Hydrogen bonds and other weak interactions in DFT. D. R. Salahub
11:30 —113. Discontinuity of the chemical potential in reduced-density-matrix-functional theory. E. Gross, N. Helbig, N. Lathiotakis
Section B
Georgia World Congress Center -- B305
8:30 —7. Profiling protein kinase substrate specificity using peptide arrays. B. E. Turk
9:10 —8. Regulation of protein motions in MAP kinases. N. Ahn
9:50 —9. Surrogate approaches to AGC-kinase inhibition. D. Bossemeyer, M. Gassel, S. Bonn, C. B. Breitenlechner, R. A. Engh
10:30 — Intermission.
10:40 —10. Processing conformation of MAP kinases. E. J. Goldsmith, T. Zhou
11:20 —11. A structural view of the protein kinase family and family-based drug discovery. S -H. Kim, J. Hou, C. Zhang
12:00 —12. A switched electrostatic network guides Src conformational activation. E. Ozkirimli, C. Post
Section C
Georgia World Congress Center -- B306
8:40 —13. Analytical electrostatics: Beyond the generalized Born model. A. Onufiev
9:05 —14. Calculating free energies with fast implicit solvent models. J. Michel, R. D. Taylor, M. L. Verdonk, J. W. Essex
9:30 —15. Modeling polarization in MD. D. M. Elking
9:55 —16. Metadynamics study of the free energy surfaces of the
alanine dipeptide in vacuum and in water: How do molecular mechanics
force fields affect backbone conformational transition of proteins and
peptides? Z. Liu, P. B. Moore, B. Ensing
10:20 — Intermission.
10:35 —17. Implementation of SCC-DFTB in AMBER. G. D. M. Seabra, R. C. Walker, A. E. Roitberg
11:00 —18. Molecular dynamics integration and molecular vibrational theory. D. Janezic
11:25 —19. Computational methods for the enhanced calculation of time-correlation functions. I. Andricioaei
11:50 —20. Multi-mode molecular dynamics and QM/MM methods for binding affinity estimation of metalloprotein ligands. A. Khandelwal, S. Balaz
Section A
Georgia World Congress Center -- B304
1:30 —21. Exact exchange as a component of density functional approximations. J. Perdew, V. Staroverov, G. Scuseria, J. Tao
2:00 —22. New density functionals applied to old problems. G. E. Scuseria
2:30 —23. Use of the adiabatic connection for constructing exchange-correlation functionals in density functional theory. P. Mori-Sánchez, A. J. Cohen, W. Yang
3:00 —24. Spin-current density-functional methods. A. Goerling
3:30 — Intermission.
3:40 —25. Advances in orbital-free density functional theory and its applications. E. A. Carter
4:10 —26. Orbital-corrected orbital-free density functional theory. B. Zhou, Y. A. Wang
4:40 —27. Recent developments in conceptual density functional theory. P. Geerlings, F. De Proft
Section B
Georgia World Congress Center -- B305
1:30 —28. Processive phosphorylation of splicing factors. J. A. Adams
2:10 —29. Conformational energy landscape of Src kinase activation processes. B. Roux, N. K. Banavali
2:50 — Intermission.
3:00 —30. Conformational changes in protein loops and helices induced by post-translational phosphorylation. M. P. Jacobson, E. S. Groban, A. Narayanan
3:40 —31. Simple models for protein kinases and their interactions with small molecule inhibitors. A. H. Elcock
4:20 —32. Classification of the human kinome based on active site features and small molecule interaction profile. K. Nam, R. P. Sheridan, V. N. Maiorov
Section C
Georgia World Congress Center -- B306
1:00 —33. Electron and proton affinities of the 3d-block transition metals using quantum Monte Carlo methods. A. A. Gibson, F. Fayton Jr., J. A. Harkless
1:25 —34. Ab initio determination of chiroptical properties. M. L. Abrams, T. D. Crawford
1:50 —35. Analysis and development of basis sets for optimal ab initio and density functional performance. A. K. Wilson, B. P. Prascher, B. Mintz, X. Wang
2:15 —36. Efficient treatment of electronic structure in highly-correlated molecular systems. G. J. Beran, M. P. Head-Gordon
2:40 —37. A first-principles method for open systems. G. Chen, X. Zheng, F. Wan
3:05 — Intermission.
3:20 —38. Analytic energy derivatives for the locally projected methods: Theory and applications. R. Z. Khaliullin, A. T. Bell, M. Head-Gordon
3:45 —39. Effective computational cost reduction via basis set truncation: Extended systems. B. Mintz, A. Shah, A. K. Wilson
4:10 —40. Scaling of GAMESS quantum chemistry calculations on a small COTS cluster. S. J. Kirkby
4:35 —41. The correlation-consistent Composite Approach (ccCA). N. DeYonker, T. R. Cundari, A. K. Wilson
5:00 —42. Calculation of acid dissociation constants by the SM6 quantum mechanical implicit solvation model. C. P. Kelly, C. J. Cramer, D. G. Truhlar
Section A
Georgia World Congress Center -- B304
8:20 —43. Ab initio density functional theory: The seamless connection with wavefunction theory. R. J. Bartlett, I. Schweigert, V. Lotrich, D. Bokhan
8:50 —44. New density functionals for electronic structure and dynamics. R. Baer, Y. Kurzweil, D. Neuhauser
9:20 —45. Some progress in DFT: Efficiency, accuracy and open system. G. Chen
9:50 —46. Subsystem functionals: A path to improved functionals. A. E. Mattsson, R. Armiento
10:20 — Intermission.
10:30 —47. Exchange-correlation functional for organometallic,
inorganometallic, and nonmetallic bonding, noncovalent interactions,
and reaction barriers. D. G. Truhlar, Y. Zhao, N. E. Schultz
11:00 —48. Mixed relativistic and non-relativistic DFT calculations for large systems containing heavy elements. L -M. Li, X -Q. Hu, F. Wang
11:30 —49. Density functional methods and vibronic interactions: Lessons from computational studies of DMX-. A. I. Krylov
Section B
Georgia World Congress Center -- B306
8:30 —50. Structure based optimization of cyclin dependant kinase inhibitors. C. McInnes
9:10 —51. Docking studies to advance the discovery and optimization of kinase inhibitors. M. L. Lamb
9:50 — Intermission.
10:00 —52. Design of selective protein inhibitors using PASSA and PAS-Dock. K. Tondel, E. Anderssen, F. Drablos
10:40 —53. Regulatory subunit RI-alpha and PKA: Allostery and dynamic binding. J. Gullingsrud, C. Kim, S. S. Taylor, J. A. McCammon
11:20 —54. Biasing for favored substituents in kinase library design. F. Soltanshahi, Q. Liu, R. D. Clark
Section C
Georgia World Congress Center -- B305
8:15 —55. Understanding hits and decoys in molecular docking. B. Shoichet, R. Brenk, S. Boyce
8:45 —56. Finding inhibitors of protein association by ICM docking into induced surface pockets. R. Abagyan, S. Saldanha, M. Totrov, M. Mallya, R. L. Phillips, D. Lomas
9:15 —57. Use of negative data in the refinement of scoring functions for virtual screening. A. N. Jain, T. A. Pham
9:45 — Intermission.
10:00 —58. Accurate prediction of ligand-receptor binding energies. B. W. Sherman, R. Farid, M. P. Repasky
10:30 —59. Validation of quantum-mechanical docking and scoring procedures. V. M. Anisimov
11:00 —60. Better knowledge – better scoring: Tailoring
DrugScore to a particular protein yields improved pose and affinity
predictions and allows to incorporate conformational variability. H. Gohlke, S. Radestock, B. Breu
11:30 — Panel Discussion.
Section D
Georgia World Congress Center -- B307
8:20 —61. Assembling the small ribosomal subunit in silico: A novel approach to determine binding interdependencies. K. Hamacher, J. Trylska, J. A. McCammon
8:45 —62. Exploring the assembly of the 30S ribosomal subunit. J. Trylska, J. A. McCammon, C. L. Brooks III
9:10 —63. Conformational change of the methionine 20 loop of
Escherichia coli dihydrofolate reductase modulates protonation of the
substrate dihydrofolate. I. V. Khavrutskii, D. J. Price, J. Lee, C. L. Brooks III
9:35 —64. Deprotonation of solvated formic acid from Car Parrinello molecular dynamics plus the novel metadynamics method. J -G. Lee, E. K. Asciutto, V. Babin, C. Sagui, T. Darden, C. Roland
10:00 — Intermission.
10:15 —65. Understanding the decarboxylation mechanism of N-carboxy-2-imidazolidinone, a Car-Parrinello molecular dynamics investigation. M. E. McKenzie, B. Chen
10:40 —66. QM/MM model of the O2-evolving complex of photosystem II. E. M. Sproviero, J. A. Gascon, J. P. McEvoy, G. W. Brudvig, V. S. Batista
11:05 —67. Modeling the key recognition event at the heart of the immune response. S. Wan, P. V. Coveney, D. R. Flower
11:30 —68. Multi-configuration molecular mechanics based on combined quantum mechanical and molecular mechanical calculations. H. Lin, Y. Zhao, D. G. Truhlar
11:55 —144. Solvent polarization and kinetic isotope effects in
nitroethane deprotonation and implications to the nitroalkane oxidase
reaction. D. T. Major, D. M. York, J. Gao
Section A
Georgia World Congress Center -- B304
1:30 —69. Early days of DFT with RGP, and a general theory of hybrids. M. Levy, A. Cohen, P. Mori-Sanchez, W. Yang
2:00 —70. Importance of the exchange-correlation potential in Kohn-Sham theory. D. J. Tozer
2:30 —71. Kohn-Sham calculations without density functionals. P. Gori-Giorgi, A. Savin
3:00 —72. Assessment of exchange-correlation functionals from the adiabatic connection. A. J. Cohen, P. Mori-Sánchez, W. Yang
3:30 — Intermission.
3:40 —73. A new hybrid DFT functional: Accurate description of response properties and van der Waals interactions. K. Hirao
4:10 —74. Density scaling and a generalized Kohn-Sham scheme. A. Nagy
4:40 —75. Time-dependent density functionals derived from variational functionals of the Green function. R. van Leeuwen
Section B
Georgia World Congress Center -- B305
1:30 —76. Progress in Computer-Aided Drug Design. W. L. Jorgensen
2:00 —77. BACE: Accounting for flexibility in a scoring Function. G. McGaughey, B. Feuston, S. Graham, M. K. Holloway, S. Lindsley, P. Nantermet, H. Rajapakse, S. Stauffer
2:30 —78. Pharmacophore-based virtual screening. J. Van Drie
3:00 — Intermission.
3:15 —79. A comparison of structure-based and shape-based tools for virtual screening. P. C. D. Hawkins
3:45 —80. PubChem: An information resource linking chemistry and biology. S. Bryant
4:15 —81. Beyond PEST descriptors: Binding site and ligand shape/property fingerprints. C. M. Breneman, C. M. Sundling, N. Sukumar, K. P. Bennett, M. J. Embrechts, S. Cramer
4:45 — Panel Discussion.
Section C
Georgia World Congress Center -- B306
1:00 —82. Wave-packets and density matrices: Using DFT for ab initio dynamics. S. S. Iyengar
1:25 —83. Dopant effects on excited states of a novel photocatalyst: A QM/MM study of ETS-10. A. M. Zimmerman, M. Nash, D. J. Doren, R. F. Lobo
1:50 —84. Models and mechanisms of the DNA (6-4) photoproduct repair by (6-4) photolyase. C. Harrison, O. Wiest
2:15 —85. Unconventional Catalytic Mechanism for histone deacetylase suggested by a DFT-QM/MM study. C. Corminboeuf, P. Hu, M. E. Tuckerman, Y. Zhang
2:40 —86. Theoretical studies on farnesyl cation cyclization: pathways to pentalenene and diversions to other natural products. P. Gutta, D. J. Tantillo
3:05 — Intermission.
3:20 —87. Theoretical studies of intramolecular hydrogen bonding in malonamide derivatives. J. N. Woodford
3:45 —88. The molecular properties of electronically excited states. C. E. Smith, T. D. Crawford
4:10 —89. Time-dependent density functional theory calculations of the electronic excited states of tryptophan in proteins. J. D. Hirst
90. Withdrawn.
4:35 —91. Computing physical properties of simple aromatics. M. H. Kassaee, D. Keffer, W. V. Steele
Section A
Georgia World Congress Center -- Ex. Hall B48:00 - 10:00
150, 156, 158, 161, 163, 166, 171-172, 180-183, 186, 190-191, 202, 208-210, 212, 214, 220-222, 224, 228, 239, 252. See subsequent listings.
Section A
Georgia World Congress Center -- B304
8:20 —92. Kinetic approach to electron transport in nanoscale devices. R. Car
8:50 —93. Advances in formal and practical time-dependent density-functional theory. S. Hirata
9:20 —94. Excited-state spin-contamination in time-dependent density-functional theory for molecules with open-shell ground states. M. E. Casida, A. Ipatov
9:50 —95. Nonperturbative treatment of atomic and molecular
multiphoton processes in intense laser fields: Self-interaction-free
TDDFT approaches. S -I. Chu
10:20 — Intermission.
10:30 —96. The application of TDDFT to systems with a spin or space degenerate ground state. T. Ziegler, M. Seth, F. Wang
11:00 —97. Time-dependent relativistic density functional theory and applications. W. Liu
11:30 —98. Quantum defect and time-dependent density functional theory. K. Burke, M. van Faassen, A. Wasserman
Section B
Georgia World Congress Center -- B305
8:30 —99. Exploration of GPCRs: Structure and function. K. Palczewski
9:00 —100. Crystal structures of rhodopsin. J. Ballesteros, K. Palczewski
9:30 —101. High throughput membrane protein structure determination by electron crystallography. H. Stahlberg, Z. Y. Zhang, B. Gipson, R. Hill, H -T. Chou, P -L. Chiu, L. Renault, X. Zeng
10:00 — Intermission.
10:15 —102. Protein interactions in GPCR signaling: A very moving story. H. Weinstein
10:45 —103. G Protein coupled receptors: Structure, ligand recognition, and receptor activation. L. Pardo
11:15 —104. Modeling ligand interactions at adenosine and P2Y nucleotide recptors: Influence of ribose conformation. K. A. Jacobson, S -K. Kim, A. A. Ivanov, S. Costanzi
Section C
Georgia World Congress Center -- B306
8:30 —105. Novel methods for modeling aluminum nanoclusters. M. Iron
8:55 —106. Computational design of an enzyme mutant for anti-cocaine medication. D. Gao, W. Yang, Y. Yang, H -H. Tai, C -G. Zhan
9:20 —107. Effects of tautomerism and hydration on the speciation of molecules: A study using SPARC. S. N. Ayyampalayam, L. Carreira
9:45 —108. Interaction of Protegrin-1 (PG-1) with lipid bilayers: Membrane thinning effect. H. Jang, B. Ma, T. B. Woolf, R. Nussinov
10:10 — Intermission.
10:25 —109. A minimal model for stabilization of biomolecules by hydrocarbon cross-linking. K. Hamacher, A. Hübsch, J. A. McCammon
10:50 —110. Metadynamics molecular simulations with accurate
quantum chemistry calculation for the study of the anions forms of
Malonic Acid. E. K. Asciutto, C. Sagui
11:15 —111. Replica exchange molecular dynamics study on
aralyamide and heparin in water: Sampling effects and analysis of the
detailed binding mode. Z. Liu, V. Pophristic
11:40 —112. Replica-exchange molecular dynamics simulations of protein adsorption on a hydrophobic surface. Y. Sun, R. A. Latour
Section A
Georgia World Congress Center -- B304
1:30 —6. Density functional theory for non-equilibrium systems. M. Ernzerhof
2:00 —114. A canonical transformation theory for multireference problems. G. K. Chan, T. Yanai
2:30 —115. Quantum phase space and the local virial theorem. L. Cohen
3:00 —116. Stress tensor in the standard model of elementary
particles and the origin of the electronic spindle structure of
chemical bond. A. Tachibana
3:30 — Intermission.
3:40 —117. Designing molecules by optimizing potentials. D. N. Beratan
4:10 —118. New computational strategies for density functional calculations. R. J. Harrison, A. Beste
4:40 —119. Using Density functional theory, new algorithms and computer simulation to probe biophysical, materials and chemical systems. G. Martyna
Section B
Georgia World Congress Center -- B305
1:30 —120. How bilayers cope with transmembrane helices: Insights from translocon-assisted helix insertion. S. H. White
2:00 —121. Ab initio modeling of the loops in G-protein coupled receptors. E. L. Mehler
2:30 —122. Studying the photochemistry of retinal proteins with quantum chemical methods. M. Elstner
3:00 — Intermission.
3:15 —123. Models for the GPCR proton sensors OGR1, GPR4, and TDAG8. R. M. Wolf, M -G. Ludwig, K. Seuwen
3:45 —124. Binding site sxpansion and induced fit docking for
GPCR ligand binding mode prediction: Application to the b-adrenergic
and chemokine receptors. A. Tebben, S. R. Kimura, P. H. Carter, Q. Zhao, S. R. Krystek Jr.
4:15 —125. The molecular basis of antagonist binding to CCR1: Molecular modeling and experiment. S. K. Schlyer,
R. Horuk, S. Koovakkat, M. J. Kochanny, R. Trabanino, W. A. Goddard
III, R. Abrol, W. B. Floriano, J. Pease, J. Fox, F. Lopez de Mendoca,
S. Sharma, V. Nagarajan
Section C
Georgia World Congress Center -- B306
1:30 — Introductory Remarks.
1:40 —126. Toward a force field based on density fitting. G. A. Cisneros, J -P. Piquemal, N. Gresh, T. A. Darden
2:20 —127. Assigning the protonation states of the key aspartates in β-secretase using QM/MM X-ray structure refinement. N. Yu, K. M. Merz Jr.
3:00 — Intermission.
3:20 —128. Virtual screening: The king (quite often) has no clothes. R. C. Glen, A. Bender
4:00 —129. Iterative focussed screening using Random Forest: A comparison with HTS/random screening for two extreme cases. C. I. Bayly, C. Brideau, A. Liaw, V. Svetnick
4:40 — Award Announcement.
Section D
Georgia World Congress Center -- B307
1:20 —130. Solvation studies by DFT of Carbohydrates: a/b-anomeric ratios of epimers of glucose using a continuum-solvation model (COSMO). U. Schnupf, J. L. Willett, F. A. Momany
1:45 —131. Molecular modeling insights into the catalytic mechanism of a family 38 glycosyl hydrolase, Golgi α-mannosidase II. S. P. Kawatkar, G -J. Boons, R. J. Woods
2:10 —132. Modeling of complex hydrides: Lattice anomaly in NaAlH4. J. Ojwang', G. J. Kramer
2:35 —133. Solvation of bihalide anions with water. D. D. Kemp, M. S. Gordon
3:00 — Intermission.
3:15 —134. Theoretical study of solvation of NaOH. P. Arora, M. S. Gordon
3:40 —135. Cyanogen and diacetylene dimer potential energy surfaces: New π--π prototypes. B. W. Hopkins, G. S. Tschumper
4:05 —136. Structural and vibrational properties of boron nitride (BN) analogs of diamondoids. S. L. Richardson, K. Park, T. Baruah, M. R. Pederson
4:30 —137. Silica-supported silver salt for paraffin/olefin separation: A DFT study. D. E. Jiang, B. G. Sumpter, S. Dai
4:55 —138. Importance of basis set construction in density functional theory. B. P. Prascher, A. K. Wilson
Section A
Georgia World Congress Center -- Ex. Hall B46:00 - 8:00
139. Conformational study of small molecules in the protein environment. I. Weidlich, M. C. Nicklaus
140. Flexible docking of the inhibitors into Tyrosyl-DNA Phosphodiesterase (Tdp1) active sites. I. Weidlich, M. C. Nicklaus
141. Computational modeling of kinases. D. J. Smith, W. Duan, C. S. Verma
142. Novel empirical free energy function for use in the protein-protein docking problem. J. Audie
143. Withdrawn.
145. A line integral reaction path approximation for large
systems via nonlinear constrained optimization: Application to alanine
dipeptide and β-hairpin of protein G. I. V. Khavrutskii, R. Byrd, C. L. Brooks III
146. Absence of aromaticity at residue 6.44 contributes to cannabinoid CB2 receptor constitutive activity. R. C. Serbanescu, J. Barnett-Norris, R. Zhang, T -K. Kim, Z -H. Song, P. H. Reggio
147. Absolute binding free energy calculation for theophylline and its analogs to RNA aptamer using BAR method with GAFF. Y. Tanida, M. Ito, H. Sato, A. Matsuura, H. Fujitani
148. Analyzing force field and charge conditions to enhance biological activity predictions of Cathepsin D inhibitors. H. N. Biles, M. W. Ellis, C. J. Collar, L. Fabry-Asztalos
149. Atomistic simulations of carbon dioxide diffusion within zeolites. D. Kohen, D. S. Davis
150. Better than RMSD: Faster methods for conformer comparison. J. J. Yang
151. Biomolecular electrostatic potential: An analytical approach. A. T. Fenley, J. C. Gordon, A. V. Onufriev
152. Computational analysis of conformational diversity of FLPs neuropeptides. G. Leonis, A. E. Roitberg
153. Computational methods for the analysis of small angle scattering spectra. J. E. Curtis, W. Ratcliff II, S. Krueger
154. Computational studies into the mechanism of human tyrosyl-DNA phosphodiesterase. B. E. Richardson, A. C. Goren
155. Computational studies of asymmetric organocatalysis. D. J. Harriman, G. Deslongchamps
156. Computational tools for LIPID metabolite and pathways strategy. M. Sud, E. Fahy, R. Byrnes, D. Cotter, A. Maer, Y. Zhao, S. Subramaniam
157. Computer simulations of glycolytic enzyme/enzyme association and implications for substrate binding. V. F. Waingeh, I. V. Ouporov, K. A. Thomasson
158. Computer-aided molecular design of Histone Deacetylase Class I inhibitors. E. X. Esposito, G. R. Cook
159. Conformational analysis of a GBR 12909 analog. C. A. Venanzi, D. Pandit, J. Naik, S. Abraham
160. Conformational sampling and folding in polyalanine peptides. S. Kim, A. E. Roitberg
161. Contributions of conformational flexibility to Brugia
malayi asparaginyl-tRNA synthetase specificity for inhibitors
identified by structure-based screening. S. C. K. Sukuru, T. Crepin, J. C. Morris, M. Grotli, F. Danel, M. G. P. Page, M. Haertlein, S. Cusack, M. A. Kron, L. A. Kuhn
162. Crystal-GA: A program for crystal structure determination via X-ray powder diffraction data. H. Arman, C. W. Padgett, W. T. Pennington
163. Cyclopentane: Forcefield and molecular dynamics analysis. A. T. Swann, P. J. Ludovice
164. De novo structure-based design of tris-urea tripodal and macrocyclic anion receptors. V. Bryantsev, B. P. Hay
165. Design of novel enzyme catalysts: Combining the benefits of quantum mechanics, rational design and directed evolution. X. Zhang, T. M. Handel, A. Chowdry
166. Detection of hidden sequence propensity for amyloid fibril formation using support vector machine. Q. Zhang, W. J. Welsh
167. Development of quantitative structure-activity relationship
models of Sodium/Potassium ATPase inhibition by cardiac glycosides. D. Rothgeb, S. Paula
168. Differential DNA-binding by some Rel/NF-κB proteins: Molecular dynamics of a κB DNA element. C. Mura, J. A. McCammon
169. Distance dependence of flurbiprofen and dapsone in the CYP 2C9 active site as studied by molecular dynamics. J. S. Aguilar, Z. R. Hartman, A. G. Niehaus, P. M. Gannett
170. Docking and molecular dynamics studies of copper containing enzyme diamine oxidase. M. R. Flaherty, S. Aditya, F. Ryvkin
171. Dramatically different structural strategies to achieve the
same metabolic goal: Molecular modeling comparison of CYP6B8v1 and
CYP321A1. T -L. Chiu, Z. Wen, M. A. Schuler
172. Effects of the L100I and L100I+K103N mutations on the
binding of etravirine analogs to HIV-1 reverse transcriptase based on
Monte Carlo simulations. T. M. Lyons, J. Tirado-Rives, W. L. Jorgensen
173. Errors in gel acrylamide electrophoresis due to effect of charge. K. R. Sharma
174. Evaluation of loop prediction protocols. C. A. Weigelt, K. A. Rossi, S. R. Krystek Jr., A. Nayeem
175. Exploring the mechanism of Trypanosoma cruzi trans-sialidase. Ö. Demir, A. Roitberg
176. Feed-forward neural network models of potential sulfonamide-substituted cycloalkylpyranone HIV protease inhibitors. C. R. Bernier, B. Bhhatarai, S. Kumar, R. Garg
177. First principles molecular dynamics simulations of benzene in water. F. C. Lightstone, E. R. Schwegler, M. Allesch, G. Galli
178. Free energy calculation from non-equilibrium simulations. H. Xiong, H -P. Cheng, A. E. Roitberg
179. Free energy profiles of DNA unzipping under tension and torque. E. C. Brunk, I. Andricioaei
180. Guiding chemical reaction path searches with graph theory. B. W. Hopkins, G. S. Tschumper
181. Hydrophobic-aided replica exchange: An efficient algorithm for sampling biological systems in explicit solvent. X. Huang, P. Liu, R. Zhou, B. Berne
182. Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model. A. Okur, L. Wickstrom, M. M. Layten, K. Song, V. Hornak, C. Simmerling
183. Improvements in predictive ADMET modeling stemming from atomic partial charges obtained by a new empirical method. R. Fraczkiewicz, G. Fraczkiewicz, M. B. Bolger, W. S. Woltosz
184. Influence of structural characteristics over the cytotoxic and hepatoprotective activities of cucurbitacin analogs. J. Bartalis, F. T. Halaweish
185. Investigation of HIV protease cyclic urea inhibitors using computational approach. D. Patel, B. Bhhatarai, R. Garg
186. Ligand-based approach for the identification of novel
inhibitors: Application to Salvinorin A, a selective kappa opioid
receptor (KOP) agonist. N. Singh, G. Chevé, S. Narayanan, C. R. McCurdy
187. Ligand-docking-based homology model of the melanin-concentrating hormone 1 receptor. A. J. Orry, C. N. Cavasotto
188. Limitations in the modeling of physical properties using the Hosoya Index. K. J. Dawson, K. McLaughlin
189. Lipid properties on nano-disc particles of Apo A-I. M. P. Aliste, S. C. Harvey
190. Modeling of human blood:air and tissue:air partition coefficients using structural descriptors. M. Kuanar
191. Modeling of peptidic inhibitors of Immunoglobulin-G degrading enzyme of Streptococcus pyogenes. J. G. Longenecker, J. P. Wolbach
192. Molecular Dynamics analysis of the interaction of Lys237 with the H-cluster of Fe-only hydrogenase. D. Dogaru, S. Motiu, V. Gogonea
193. Molecular dynamics and stochastic simulations of surface diffusion. J. M. Moix, R. Hernandez
194. Molecular dynamics simulation of conformational changes in nicotinic acetylcholine receptor triggered by agonist binding. X. Cheng, J. A. McCammon
195. Molecular dynamics study of hydrogen bonding interactions of dapsone and flurbiprofen within the CYP 2C9 active site. Z. R. Hartman, J. L. Fry, B. L. Gardner, J. S. Aguilar, P. M. Gannett
196. Molecular modeling of phase behavior and microstructure of acetone-chlorforom-methanol binary mixtures. G. K. Kamath, J. J. Potoff
197. Molecular modeling, circular dichroism and FTIR studies of
conformation adopted by tetrapeptides with inhibitory activity for
thrombin. C. Clement, C. Matthaeus, M. Philipp
198. Molecular modeling studies of novel cyclic urea HIV protease inhibitors. D. Patel, R. Garg
199. On the derivation of a damped wave transport equation from Spring-Dashpot viscoelastic model. K. R. Sharma
200. On the second law violation in Fourier heat conduction. K. R. Sharma
201. On the use of cutrices in restriction mapping of three enzymes. K. R. Sharma
202. Principal mode analysis for calculating vibrational frequencies and modes of models for the peptide bond. R. A. Wheeler, K. Brorsen, S. E. Boesch
203. Probabilistic neural networks: Predicting good HIV protease inhibitors. C. R. Bernier, B. Bhhatarai, S. Kumar, R. Garg
204. Proteomics and dimensional separation. K. R. Sharma
205. Quantum Monte Carlo simulations in high-dimensional
configuration spaces: A comparison of second- and fourth-order
propagators. B. Magnusson, R. J. Hinde
206. Rotational disorder in conjugated oligomers: A nonlinear one-dimensional configuration-coordinate model. L. Liu, M. A. Berg, D. Yaron
207. Side-chain mobility and binding selectivity of naphthylquinoline derivatives. A. Sood, M. J. Lovell, G. R. Bishop, D. H. Magers
208. Site-of-metabolism prediction: A computational model based on reactivity and P450-substrate complementarity. M. Wu, M. R. Wester, Y -A. He, D. Dalvie, B. Holwerda, R. Love, H. Parge, C. Lee, B. Burke
209. Strategies for building fullerenes and nanotubes on Spartan. J. Mann, K. Jones, T. Manning, I. Barton
210. Structural determinants of binding of small molecules to extracellular matrix: Multi-species, multi-mode 3-D-QSAR analysis. Y. Zhang, V. Lukacova, V. Bartus, S. Balaz
211. Structure-based design of reversible peptides inhibitors for Factor VIIa. C. Clement, L. Gingold, M. Philipp
212. Understanding agonism in the NMDA receptor: Comparing NR2A and NR2D using MD. M. T. Geballe, K. Erreger, S. F. Traynelis, J. P. Snyder
213. Using QSAR techniques: Analysis of estradiolic ligand binding to the estrogen receptor. L. C. Streeter, R. Garg
214. Vibrational mode mixing analysis of a HIV-1 protease-inhibitor complex. H. Goto, T. Kmakura
215. Web-based entropic scoring functions: Advances in protein structure validation. J. Foley IV, S. Zhong, G. Ozer, R. Hernandez
216. Withdrawn.
217. Molecular dynamics simulation of the human P2Y14 receptor and study of ligand-receptor interactions. A. A. Ivanov, K. A. Jacobson
218. Systematic active site refinement of GPCR models through molecular dynamics simulation. S. R. Kimura, S. Krystek Jr., A. Tebben, D. R. Langley
219. Quantum chemical treatment of the Ene reaction activation parameters. M. Rectenwald, J. D. Evanseck
220. Quantum dynamics of [1,5] hydrogen shift in 1,3-pentadiene:
implications for kinetic isotope effects and Swain-Schaad exponents. J. D. Thoburn, D. N. Peles
221. Quantum mechanical analysis of cadmium sulfide/selenium quantum dots. J. M. Bair, J. D. Madura
222. Prediction of excited states for carbon, nitrogen and oxygen systems using quantum Monte Carlo. F. Fayton Jr., A. A. Gibson, J. A. Harkless
223. Semiempirical and QM calculations of absorbance wavelengths
of environmentally sensitive near-IR dyes for biosensor applications. D. B. Sherman, K. J. Thomas, A. Ambroise, J. B. Pitner
224. Theoretical study of the isomerization mechanism of azobenzene and symmetrically disubstituted azobenzene Derivatives. C. R. Crecca, A. Roitberg
225. Ab initio study of meta-substituted diphenyl ureas. S. Dehghan, V. M. Wurster, C. A. Capacci, R. Hiremath, J. A. Swift
226. Ab initio studies of diboracarbonyl molecules. J. L. Meeks
227. A computational study of 1,2-HBr elimination and 1,2-ClBr interchange in hydrobromocarbons and bromochlorocarbons. G. L. Heard, C. M. Olson, L. W. Friederich, B. E. Holmes
228. Stability of H2 clathrates vs. cavity occupancy. V. N. McCarthy, K. D. Jordan
229. A computational study of the barrier height of the 1,2-FCl exchange reaction of substituted ethanes. W. C. Everett, B. E. Holmes, G. L. Heard
230. The effect of chromophore conformation in green fluorescent protein on its absorption spectrum: A QM/MM and TDDFT study. S. Trohalaki, S. S. Patnaik, R. Pachter
231. Accuracy of FMO-MO for Large Scale Molecule. Y. Inadomi, H. Umeda, T. Watanabe, U. Nagashima, T. Ishimoto
232. Theoretical studies of dissociation of perfluorohydroxylamine. H. Sayin, M. L. McKee
233. Accurate proton affinity and gas-phase basicity values of molecules important in biocatalysis. K. Range, A. Moser, D. M. York
234. Theoretical studies on adduct formations of Pt (IV) and Pd (IV) complexes with an engineered oligonucleotide. M. Jeudy, B. Cardelino
235. Activation of the C-X bond by palladium: Ab initio benchmarks and evaluation of DFT. G. T. de Jong, F. M. Bickelhaupt
236. Theoretical studies on iron-substituted barium titanate perovoskite clusters. C. F. Bryant, B. Cardelino
237. Alternate mechanisms for the formation of volatile selenium species. T. R. I. Takatani, J. M. Galbraith
238. Theoretical study of the magnetic properties of quinoidal oligothiophenes. L. R. Waller, T. Waller
239. Anomeric control of high energy bonds. E. A. Ruben, M. S. Chapman, J. D. Evanseck
240. Application of FMO-MO fior Large-Scale Molecule: Effect of solvent molecules. T. Watanabe, Y. Inadomi, H. Umeda, T. Ishimoto, U. Nagashima
241. Benchmark quantum mechanical computations on the acid-catalyzed Diels-Alder reaction between butadiene and methyl acrylate. R. A. Newton, J. A. Plumley, J. D. Evanseck
242. Calculation of nuclear spin-spin coupling constants of
molecules with first and second row atoms in study of basis-set
dependence. W. Deng, J. R. Cheeseman, M. Frisch
243. Computational studies of gas and condensed phase properties of donor-acceptor complexes of sulfur trioxide. J. M. Standard, P. S. Fudacz, B. N. Ida
244. Computational study of Cadmium Sulfide with amino acids as organic capping agents. D. J. Bunk
245. Conventional ring strain in unsaturated four-membered rings. Q. Cheng, S. S. Huskey, D. H. Magers
246. Conventional strain energy and sigma delocalization in small heterocycles of carbon and germanium. L. A. Taylor, C. B. Coghlan, D. H. Magers
247. Conventional strain energy and sigma delocalization in small heterocycles of carbon and silicon. H. McAlexander, B. Magers, C. B. Coghlan, D. H. Magers
248. Conventional strain energy in boracycloproane, diboracyclopropane, boracyclobutane, and diboracyclobutane. B. Magers, H. McAlexander, D. H. Magers
249. Core-valence correlation consistent basis sets revisited for the second-row atoms (Al-Ar). S. Yockel, A. K. Wilson
250. Counter-ion effects of bis(oxazoline) copper(II) catalyzed Diels-Alder reactions. E. G. Franklin, J. DeChancie, J. D. Evanseck
251. Coupled cluster calculations of the H-/H2 potential energy and dipole moment function. P. K. Moehlen, R. J. Hinde
252. Density functional theory study on the mechanism of the ribosome. H. Liu
253. Development of protonic and deuteronic basis functions using Gaussian-type functions. T. Ishimoto, M. Tachikawa, Y. Inadomi, H. Umeda, T. Watanabe, U. Nagashima
254. Direct Born-Oppenheimer dynamics of the Bauld-plateau rearrangements. C. Harrison, C. Doubleday, O. Wiest
255. Disconnection of maximum stereoelectronic effects from the transition structure. J. A. Plumley, J. D. Evanseck, O. Acevedo
256. Enthalpies of formation for thio ethers by homodesmotic reactions. R. Fortenberry, D. H. Magers
257. Generalization of planar hexacoordinate carbon. K. Ito, Z. Chen, C. S. Wannere, P. V. R. Schleyer
258. Hydrogen abstraction reactions using hybrid density functional theory with specific reaction parameters. N. De Silva, S. Swaminathan, T. V. Albu
259. Investigation of metal dependent behavior of HIV-1 integrase inhibitors: DFT calculations. N. Nunthaboot
260. Investigation of the inhibition of Fe-only and Ru-modified H-cluster by molecular oxygen: A density functional theory study. S. Motiu, D. Dogaru, V. Gogonea
261. Modeling of d10 coinage-metal complex excited states. T. V. Grimes, T. R. Cundari, M. A. Omary
262. Parallel Fock matrix construction on the Grid. H. Umeda, Y. Inadomi, T. Watanabe, T. Ishimoto, U. Nagashima
263. DFTB Energy decomposition analysis of interactions in Fullerene@SWNT nanopeapods. Z. Wang, S. Irle, G. Zheng, K. Morokuma, R. Kitaura, H. Shinohara
264. Enthalpies of formation of TNT derivatives by homodesmotic reactions. A. Sood, P. L. Honea, D. H. Magers
265. Theoretical study of the electronic and geometrical structures of organic semiconductors. M. M. Bader, G. P. Gutshall, A. Scotto Di Marco, H. Lin
266. Thermodynamic studies on the effect of metal complexes, similar to those used as anticancer drugs, on an oligonucleotide. J. Stoudmire, A. R. Siler, B. Cardelino
267. N1s and C1s core electron binding energies for 2-, 3-, and
4-substituted pyridines calculated by density functional theory (DFT):
Correlations with Hammett substitutent constants. Y. Takahata
268. Philicity concept revisited. P. K. Chattaraj, U. Sarkar, D. R. Roy, R. Parthasarathi, J. Padmanabhan, V. Subramanian
269. Spin-Potential functional formalism for current-carrying noncollinear magnetic systems. T. Heaton-Burgess, P. W. Ayers, W. Yang
270. Confined atoms and molecules: Some new results. K. D. Sen
271. Control and monitoring of physical objects in biomolecular systems: Some novel experimental tools and theoretical models. K. Rupnik
272. Correlation energy density functionals for two-electron systems. J. Katriel, S. Roy, M. Springborg
273. EEM and Spectrophores. W. Langenaeker, H. De Winter, G. Thijs, J. Taminau
274. From coordinate space density to momentum-space density sans wave functions. R. K. Pathak
275. Fundamental importance of the Coulomb hole sum rule to understanding of the Colle-Salvetti wave function. X -Y. Pan, V. Sahni, L. Massa
276. Molecular dynamics simulations with the ABEEM force field based on density functional theory. Z -Z. Yang
Section A
Georgia World Congress Center -- B304
8:20 —277. An "atoms" in "molecules" based chemical reactivity theory. M. H. Cohen, A. Wasserman
8:50 —278. Fractional charge in diatomics-in-molecules hamiltonians. S. M. Valone, S. R. Atlas
279. Withdrawn.
9:20 —280. Chemical reactivity indexes and the auxiliary density. A. Vela
9:50 — Intermission.
10:00 —281. Link between reaction force and DFT reactivity descriptors. S. Gutiérrez-Oliva, B. Herrera, A. Toro-Labbé
10:30 —282. Role of the density response function in the interaction of a hard and a soft species. A. Cedillo
11:00 —283. Why does the Hard-Soft Acid-Base Principle work? Insights obtained by considering acid (or base) exchange reactions. P. W. Ayers
Section B
Georgia World Congress Center -- B305
8:30 —284. Beyond keeping it together: Extracellular loops in
the cannabinoid receptor and rhodopsin play a key role in receptor
stability and ligand binding. D. L. Farrens, J. F. Fay
9:00 —285. Molecular dynamics simulations of cannabinoid CB1 receptor/endogenous ligand recognition via the membrane bilayer. P. H. Reggio, D. L. Lynch
9:30 —286. Molecular dynamics simulations of the structural
stability of the cannabinoid-CB1 receptor inactive state model in a
POPC bilayer. D. L. Lynch, J. Barnett-Norris, D. P. Hurst, P. H. Reggio
10:00 — Intermission.
10:15 —287. Computational studies of G-protein coupled receptor oligomers. M. Filizola
10:45 —288. Defining the ligand binding site on the human C5a receptor. P. N. Monk, A. Higginbottom, P. K. Madala, J. D. A. Tyndall, M. Stoermer, D. P. Fairlie
11:15 —289. Inactive and active states and supramolecular organization of GPCRs: Insights from computational modeling. F. Fanelli, P. G. De Benedetti
Section C
Georgia World Congress Center -- B306
8:20 —290. Computer simulation of nano tin melting behavior: Effect of particle size and temperature ramping up rate. H. Dong, K -S. Moon, H. Jiang, C. Wong, M. I. Baskes, F. Hua
291. Withdrawn.
8:45 —292. Hydration and dewetting near fluorinated superhydrophobic plates. X. Li, J. Li, M. E. Eleftheriou, R. Zhou
9:10 —293. Mass transport of O2 and N2 in nanoporous carbon
(C168 Schwarzite) using quantum mechanical force field and molecular
dynamics simulations. G. Arora, S. I. Sandler
9:35 — Intermission.
9:50 —294. Nucleation, growth and domain formation in solid-solid phase transitions. S. Leoni, D. Zahn
10:15 —295. Nucleation and growth in the fluorite to PbCl2-type pressure-induced phase transition in CaF2. S. E. Boulfelfel, D. Zahn, O. Hochrein, Y. Grin, S. Leoni
10:40 —296. Quantitative chiral recognition in silico, from chromatography to proteins. T. Hanai
11:05 —297. The Brownian dynamics in suspension of swelling/shrinking colloids. A. Popov, R. Hernandez
Section A
Georgia World Congress Center -- B304
1:30 —298. Density functional studies of orgnometallic systems. H. F. Schaefer III
2:00 —299. Using hybrid DFT methods to understand the structure and reactivity of transition metal-dependent enzymes. N. G. J. Richards
2:30 —300. DFT and approximate SCC-DFTB methods applied to biological systems: Successes and problems. M. Elstner
3:00 —301. A DFT and QM/MM study of the active site of human DNA Polymerase Beta. L. G. Pedersen, P. Lin
3:30 — Intermission.
3:40 —302. Clusters: Structures and properties. M. S. Gordon, R. M. Olson, S. A. Varganov
4:10 —303. Development and application of density functional theory QM/MM approach to studying metalloenzymes. Y. Zhang
4:40 —304. Modeling biological reactions with density-functional theory: Multi-scale. D. York
Section B
Georgia World Congress Center -- B305
1:30 —305. Structure-based design of opioid ligands. D. M. Ferguson
2:00 —306. Predicting and understanding GPCR-ligand binding using feature-map vectors. J. E. Penzotti, G. A. Landrum
2:30 —307. Homology modeling of angiotensin II type 1 (AT1)
receptor and in silico screening in search of unique AT1 antagonists
with selective PPAR-ă modulating activity. A. Patny, P. V. Desai, M. Avery
3:00 — Intermission.
3:15 —308. Optimizing diverse combinatorial libraries around known targets. T. E. Mansley, F. Soltanshahi, R. D. Clark
3:45 —309. Large-scale ligand-based modeling for predictive drug design. A. N. Jain, A. E. Cleves
Section C
Georgia World Congress Center -- B306
1:20 —310. A computational study on the stability of new krypton-bonded molecules. S. Yockel, E. Gawlik, A. K. Wilson
1:45 —311. Activation of the C-X bond by palladium: Direct oxidative insertion vs. SN2 and the importance of relativistic and solvent effects. G. T. de Jong, F. M. Bickelhaupt
2:10 —312. Adsorption of H2S on carbon nantube. Y. Wang
2:35 —313. Combined ab initio and ab initio molecular dynamics studies on the oxygen reduction reaction on Pt surface. Y. Wang
3:00 — Intermission.
3:15 —314. Investigation of H2 adsorption sites in MOFs using ab initio methods. C. Buda, B. D. Dunietz
3:40 —315. Quantum chemical molecular dynamics study of
single-walled carbon nanotube (SWCNT) nucleation on metal catalyst
nanoparticles Fe38/Co38/Ni38. G. Zheng, S. Irle, M. Elstner, K. Morokuma
4:05 —316. Electronic structure of oxo-Mn(salen). J. S. Sears, C. D. Sherrill
4:30 —317. Ab initio insight on the interaction of Urate with Li+, Na+, K+, Be2+, Mg 2+ and Ca2+ Metal Cations. R. N. Allen, M. K. Shukla, J. Leszczynski
4:55 —318. MFCC-DM with pairwise interaction correction for quantum chemical study of protein. X. Chen, Y. Zhang, J. Z. Zhang
Section A
Georgia World Congress Center -- B304
8:20 —319. Questionable spin parameters from DFT. E. R. Davidson
8:50 —320. Further development and applications of the DFTB (Density Functional Tight Binding) method. K. Morokuma
9:20 —321. Hydrogen-bonded clusters. A. J. Thakkar
9:50 —322. Density functional theory of materials modeling at different length scales. S. K. Ghosh
10:20 — Intermission.
10:30 —323. Chemical accuracy along reaction paths: Full
ab-initio calculation of the full vibrational spectrum of the fluorine
molecule to wavenumber accuracy. K. Ruedenberg, L. Bytautas, T. Nagata, N. Matsunaga, M. S. Gordon
11:00 —324. Solving the Schrödinger and Dirac-Coulomb Equations and developing the Giant SAC/SAC-CI Method. H. Nakatsuji
11:30 — Concluding Remarks. Robert G. Parr.
Section B
Georgia World Congress Center -- B305
8:20 — Introductory Remarks.
8:25 —325. A DFT study of the action of Vitamin K Carboxylase. L. G. Pedersen, C. H. Davis
8:55 —326. Did amyloid seed the origins of life? D. Lynn, A. Mehta, K. Lu, J. Dong, Y. Liang, P. Liu, R. Ni, W. S. Childers, J. Simmons, S. Dublin
9:25 —327. Development of diffusion ordered NMR spectroscopy: Promise and pitfalls. C. S. Johnson Jr.
9:55 —328. Molecular modeling of the oxidized form of nuclear
factor κB suggests a mechanism for redox regulation of DNA binding and
transcriptional activation. E. W. Taylor, V. Chandrasekaran
10:25 —329. Molecular Skeleton Analysis (MoSA) and its application for NMDA/glycine/kynurenic binding complex. G. Liang, S. Li, Y. Gu, A. Lewin, J. P. Bowen
10:55 —330. QSAR studies of high potency sweeteners and novel sweetener discovery. L. L. D'Angelo, G. A. Iacobucci
11:25 —331. Selective isotopic labeling in macromolecular NMR studies. R. E. London, S. A. Gabel, T. W. Kirby, B. Bose-Basu, E. F. DeRose, G. Gao, G. A. Mueller, W. A. Beard, S. H. Wilson
Section C
Georgia World Congress Center -- B306
8:00 —332. Successful structure-based design of novel protein tyrosine phosphatase inhibitors. M. J. Bower,
A. P. Combs, E. W. Yue, P. J. Ala, B. Wayland, B. Douty, A. Takvorian,
P. Polam, Z. Wasserman, W. Zhu, M. Crawley, J. Pruitt, R. Sparks, B.
Glass, D. Modi, E. McLaughlin, L. Bostrom, M. Li, L. Galya, K. Blom, M.
Hillman, L. Gonneville, B. G. Reid, M. Wei, M. Becker-Pasha, R. Klabe,
R. Huber, Y. Li, G. Hollis, T. C. Burn, R. Wynn, P. Liu, B. Metcalf
8:25 —333. Hierarchical representation of protein conformation: Application in flexible receptor docking. Y. Zhao, D. Stoffler, M. F. Sanner, A. Olson
8:50 —334. Homology modeling: Evaluation of loop modeling protocols. K. A. Rossi, C. A. Weigelt, S. R. Krystek Jr., A. Nayeem
9:15 —335. D2Score: A fully automated web server for the dihedral angle based analysis of protein structures. G. Ozer, J. Foley IV, S. Zhong, R. Hernandez
9:40 —336. Assessment of protein structures at the residue level using an entropic score of dihedral-angle correlation. S. Zhong, S. Quirk, R. Hernandez
10:05 — Intermission.
10:15 —337. Hinge-bending motion in S-adenosyl-L-homocysteine hydrolase: Mutagenesis, fluorescence and modeling. K. Kuczera, R. T. Borchardt, R. L. Schowen, C. K. Johnson, M. Wang, C. Hu
10:40 —338. Molecular modeling of the C-terminal end of human intestinal mucin (MUC2) predicts a cysteine-knot tertiary structure. V. D. Sadasivan, D. E. Budil, A. Sacco Jr, R. L. Carrier
11:05 —339. Prediction of Human DP Receptor Structure and Binding mode for prostanoid compounds. Y. Li, F. Zhu, N. Vaidehi, W. A. Goddard III
11:30 —340. Structural model of CCR5 for the discovery of entry inhibitors for the therapeutic intervention of HIV-1 infection. D. Das, K. Maeda, K. Tsuchiya, H. Mitsuya
Section D
Georgia World Congress Center -- B307
8:30 —341. Improved docking method for organics adsorbed in zeolite catalysts. S. S. Jirapongphan, J. Warzywoda, D. E. Budil, A. Sacco Jr.
8:55 —342. Integration of in-silico filters and computational
quantum chemistry for structure based COX-II specific drug design and
screening. R. R. Gupta, L. E. K. Achenie
9:20 —343. Modeling fragmentation reactions of gas-phase peptide-ions. C. R. Kinsinger, K. K. Irikura
9:45 —344. Molecular modeling of chemical warfare agents. G. K. Kamath, J. J. Potoff
10:10 — Intermission.
10:25 —345. Rapid and accurate evaluation of the electromagnetic response properties of noble metal nanoparticles. R. J. Hinde
10:50 —346. Reactive molecular dynamic approach to thermal decomposition of kerogen. E. Salmon, F. Lorant, F. Behar, P. Metzger, C. Largeau, A. C. van Duin, W. A. Goddard III
11:15 —347. Structural characterization of n-octanol and 3-octanol interfaces using molecular dynamic simulations. P. B. Moore, N. Z. Rao, R. L. Napoleon
11:40 —348. Optimization of ROMP poly(norbornene) as a catalyst support using molecular simulations. A. T. Swann, P. J. Ludovice
Section A
Georgia World Congress Center -- B304
1:30 —349. Computational chemistry with "MULTIMODE" and new strategies for ab initio potential energy surface . J. M. Bowman, B. Braams, S. Carter, X. Huang, Z. Jin, Z. Xie
2:00 —350. Structural features of hairpin triloops in rRNA in light of global conformational changes upon ligand binding. P. M. Mitrasinovic
2:30 —351. Molecular docking and analysis of interactions between vascular endothelial growth factor (VEGF) and SPARC protein. V. Chandrasekaran, E. W. Taylor, J. Ambati
3:00 —352. New NMR approaches to the structure of carbohydrates bound to proteins. J. H. Prestegard
3:30 —353. Recent developments and applications of the ONIOM Method. K. Morokuma
4:00 —354. Tautomerization states of pteridine analogs: Quantum mechanics calculations and 13C NMR studies. J. P. Bowen, H. Zhong
Section B
Georgia World Congress Center -- B305
1:15 —355. Using shape, chemistry and electrostatics to identify bioisosteric fragments. A. G. Skillman, R. Tolbert, A. Nicholls
1:40 —356. A new way to find the needles in a haystack: Identify promising HTS hits in SAR-bearing clusters. S. F. Yan, H. Asatryan, J. Li, Y. Zhou
2:05 —357. QSAR Data cleansing with independent component analysis. C. M. Breneman, M. J. Embrechts, L. Han
2:30 —358. Reverse fingerprinting, multiple seed similarity searching and fingerprint bit importance. C. Williams
2:55 — Intermission.
3:05 —359. Computational target validation based on 3-D QSAR for antiparasitic leads. P. Athri, R. R. Tidwell, W. D. Wilson
3:30 —360. Spectrophore technology for fast and reliable virtual screening. W. Langenaeker, H. De Winter, G. Thijs, J. Taminau
3:55 —361. Structure and binding of glycopeptide antibiotics to bacterial cell wall analogs: Solvent and dimerization effects. J -G. Lee, C. Sagui, C. Roland
362. Withdrawn.
4:20 —363. STIMD: A grid-based method for accelerating the
calculation of differences in binding free energies and its application
to the binding of peptides to Src SH2 protein domains. P. W. Fowler, S. Jha, P. V. Coveney
Section C
Georgia World Congress Center -- B306
1:30 —364. An application of QM-QSAR to predict and rationalize
the refractive index of a wide variety of simple organic/organosilicon
molecules. A. Holder, L. Ye, J. D. Eick, C. Chappelow
1:55 —365. Quantum mechanical structure-activity relationship to predict volume shrinkage. M. D. Miller, A. Holder, K. Kilway, C. Chappelow, J. D. Eick
2:20 —366. Effect of electron donating and withdrawing substituents on the ring stability of cyclobutadiene. M. W. Zakaria, S. J. Kirkby
2:45 —367. On the delocalization of electrons in donor-acceptor molecules. P. M. Mitrasinovic
3:10 — Intermission.
3:25 —368. Potential energy surface of cation-pi interaction: Quantum chemical studies. S. Dakshanamurthy
3:50 —369. On the accuracy of density functional theory for iron-sulfur clusters. R. K. Szilagyi, M. A. Winslow
4:15 —370. Quantum Monte Carlo studies of S4 conformer energetics. J. A. Harkless, J. S. Francisco
4:40 —371. To achieve stable spherical clusters: General principles and experimental confirmations. Z. Chen, S. Neukermans, X. Wang, E. Janssens, S. Roger E, R. B. King, P. V. R. Schleyer, P. Lievens
5:05 —372. Role of oxygen vacancies on growth of 1B (Au, Ag and Cu) particles on TiO2(110). D. Pillay, G. S. Hwang