|
OTHER SYMPOSIA OF INTEREST: Academic Employment Initiative (see AEI, Mon) Advances in Virtual High-Throughput Screening (see CINF, Wed, Thu) Emerging Technologies in Chemical Information (see CINF, Sun) Forging Leadership Pathways for Women in Science (see CINF, Sun) Graduate Education in Chemical Informatics: Needs and Opportunities (see CINF, Mon) Diversity and Chemogenomics (see MEDI, Mon) Molecular Modeling on an Undergraduate Budget - A Symposium in Memory of Prof. Wayne P. Anderson (see CHED, Wed) State of the Art - Rational Drug Design, Applications to Teaching (see CHED, Sun) Teaching Bioinformatics in the Undergraduate Curriculum (see CHED, Sun) Molecular Modeling in Environmental Chemistry (see ENVR, Sun) Computational Chemistry (see INOR, Wed) Computational Chemistry (see INOR, Sun) NSF Sponsored Center for Workshops in the Chemical Sciences and the Impact of the Workshops on Curriculum Development (see CHED, Wed) Integration of Analytical and Experimental Data into Enterprise-Wide Systems (see CINF, Mon) BUSINESS MEETING: Sat |
Section A
Pennsylvania Convention Center -- 109B
9:00 — Introductory Remarks.
9:05 —1. Docking with water and post-docking analysis: New developments to the GOLD docking program. J. C. Cole
9:35 —2. Identification of novel p38 MAP kinase inhibitors using new Glide docking and scoring algorithms. T. A. Halgren, L. L. Frye, J. R. Greenwood, R. B. Murphy, R. A. Friesner
10:05 —3. Docking and scoring: Improvements in screening enrichment and docking accuracy. A. Jain
10:35 — Intermission.
10:45 —4. Modeling correlated protein main-chain and side-chain motions in ligand docking and screening. L. A. Kuhn, M. I. Zavodszky, S. Arora, M. Lei, M. F. Thorpe
11:15 —5. Docking conformationally flexible molecules with MVP. M. H. Lambert
11:45 —6. Scoring functions: What works and what doesn't. M. McGann
12:15 — Concluding Remarks.
Section B
Pennsylvania Convention Center -- 104A&B
8:20 —7. Biased torsional mutations and their role in conformational GA. A. Strizhev, R. D. Clark, E. Abrahamian, P. R. N. Wolohan
8:40 —8. Application of QM-QSAR method to predict mutagenicity of dental monomer. A. J. Holder, L. Ye, E. Kostoryze, C. Chappelow, J. D. Eick
9:00 —9. On the role of fluorine in intermolecular interactions. S. Mecozzi
9:20 —10. Possible regions of fullerene self-assembly in laser-produced plasma. P. M. Mitrasinovic
9:40 —11. Halide ions in a "methyl pocket": Competition between hydrogen bonding and ion-dipole interactions. Q. K. Timerghazin, T. N. Nguyen, G. Peslherbe
10:00 —12. From philosophy of computational quantum chemistry to philosophy of computational biology. B. Ma
10:20 —13. Integrated web-based grid-computing environment for research and collaboration in computational science and engineering. T. N. Truong
10:40 —14. Theoretical study of atmospherically important complexes of Criegee intermediate with water clusters and its reactions. A. Ryzhkov, P. Ariya
11:00 —15. Family 18 chitolectins: Comparison of MGP40 and GP39. P. Dalal, J. D. Madura, N. N. Aronson Jr.
11:20 —16. Chiral recognition by silver: A Q2MM study. E. Kieken, O. Wiest, P. Helquist, P. O. Norrby
11:40 —17. Nanoscale manipulation of hydrogen storage in NaAlH4: Exploring catalytic surfaces using density functional theory. S. Chaudhuri, P. Liu, J. T. Muckerman
12:00 —18. DFT study of the interactions of antiwear additives with iron and iron oxide. H. Wen, S. M. Opalka, C. V. Cooper
Section A
Pennsylvania Convention Center -- 109B
1:30 — Introductory Remarks.
1:35 —19. Methods of consensus scoring for in silico screening. K. M. Branson, B. J. Smith
2:05 —20. Can we learn from active ligands to improve the efficiency of virtual screening? The BHB scoring function. M. Feher, E. Deretey, S. Roy
2:35 —21. Native atom types for knowledge-based potentials: Application to binding energy prediction. B. N. Dominy, E. Shakhnovich
3:05 —22. SAR-directed docking. G. Skillman, S. Wlodek, M. Stahl, A. Nicholls
3:35 — Intermission.
3:45 —23. Modeling the active site of β-secretase: Application to drug discovery. R. Rajamani, C. H. Reynolds
4:15 —24. Evaluating scoring functions for docking and designing β-secretase inhibitors. M. K. Holloway,
J. C. Culberson, J. Shpungin, S. Munshi, C. A. Coburn, S. J. Stachel,
K. G. Jones, E. Loutzenhiser, A. R. Gregro, M. T. Lai, M. C.
Crouthamel, B. L. Pietrak
4:45 —25. Improving docking enrichments by picking "the right pose". H. E. Purkey, E. Evensen, K. E. Lind, E. K. Bradley
5:15 — Concluding Remarks.
Section B
Pennsylvania Convention Center -- 104A&B
1:30 —26. Scalable second-order Moller-Plesset linear R12 method with non-exact HF orbitals. E. F. Valeev, C. L. Janssen
1:50 —27. Self-consistent relativistic density functional calculations including scalar and spin-orbit effects. J. E. Peralta, G. E. Scuseria
2:10 —28. Systematic improvement of approximate density functionals. V. N. Staroverov, G. E. Scuseria, J. P. Perdew, J. Tao, E. R. Davidson
2:30 —29. Transition metal chemistry: A step toward high accuracy description of structural and energetic properties. A. K. Wilson, P. Sinha, M. A. Omary, P. S. Bagus
2:50 —30. Nth-order derivatives of nuclear attraction integrals (NAIs) and electron repulsion integrals (ERIs). F. W. Aquino, J. H. Rodriguez
3:10 —31. On emerging fields of quantum chemistry at finite temperature. L. Wei
3:30 —32. Hybrid density functional studies of bulk actinide oxides. I. D. Prodan, K. N. Kudin, R. L. Martin, G. E. Scuseria
3:50 —33. Computational study of the C-H bond dissociation enthalpies and radical reactions with substituted ethylenes and benzenes. J. K. Merle, C. M. Hadad
4:10 —34. Correlation energy extrapolation by intrinsic scaling. L. Bytautas, K. Ruedenberg
4:30 —35. Computational estimates of the gas-phase basicities and proton affinities of the six isomers of dihydroxybenzoic acid. F. H. Yassin, D. S. Marynick
4:50 —36. Activation of the alpha carbon of an
alpha,beta-unsaturated carbonyl compound toward nucleophilic attack: An
experimental and theoretical study. D. C. Chatfield, E. Lewandowska, A. Gairola, C. D'Cunha, C. Alvarez
5:10 —37. Ab initio studies of methyl and t-butyl group motions in aromatic molecular solids. X. Wang, P. A. Beckmann, F. B. Mallory, M. M. Francl
Section C
Pennsylvania Convention Center -- 106A&B
1:30 — Introductory Remarks.
1:40 —38. Near-neighbor net MD: A perturbation method for non-additive Hamiltonians. L. V. Woodcock
2:05 —39. Calculation of the binding affinities for
Stromelysin-1 (MMP-3) inhibitors using a linear scaling semi-empirical
quantum chemistry method. J. Li, C. H. Reynolds
2:30 —40. A new hybrid explicit/implicit solvent method for biomolecular simulations. M. S. Lee, M. Olson
2:55 — Intermission.
3:10 —41. ALL-QSAR: A novel automated lazy aearning QSAR Approach and its application to experimental datasets. S. Zhang, A. Golbraikh, A. Tropsha
3:35 —42. Automated Bayesian neural network modeling for chemists: Creating local models. N. R. McElroy, P. Bruneau
4:00 —43. Discovering cause-and-effect models in small formulation data sets using neurofuzzy logic. E. A. Colbourn, S. J. Roskilly, R. C. Rowe
4:25 — Awards Presentation.
Section A
Pennsylvania Convention Center -- 109A
9:00 — Introductory Remarks.
9:05 —44. FlexX-Docking: Past, present and planned technological advancements. C. Lemmen, S. A. Hindle, M. Gastreich, I. Dramburg, H. Claußen
9:35 —45. Importance of accurate docking for potency prediction. C. McMartin
10:05 —46. Recent advances in AutoDock: Search, representation and scoring. G. M. Morris, R. Huey, W. Lindstrom, C. Li, Y. Zhao, W. E. Hart, R. Belew, M. F. Sanner, D. S. Goodsell, A. J. Olson
10:35 — Intermission.
10:45 —47. Model systems for docking. B. Shoichet
11:15 —48. Enhanced ligand docking and scoring with LigandFit. C. M. Venkatachalam, J. Jiang, A. Krammer, M. Waldman
11:45 —49. Ehits: Exhaustive flexible ligand docking with customizable scoring function tailored to protein families. Z. Zsoldos
12:15 — Concluding Remarks.
Section B
Pennsylvania Convention Center -- 104A&B
9:00 — Introductory Remarks.
9:30 —50. Bonding ideas out of calculations. R. Hoffmann
10:00 —51. MO crossings in cycloaromatization reactions. I. V. Alabugin
10:30 —52. In pursuit of subchemical accuracy in computational thermochemistry. W. D. Allen, M. Schuurman, S. Wheeler, J. P. Kenny, H. F. Schaefer III
11:00 —53. Two-component approach to molecular parity violation. R. Berger, C. van Wüllen
11:30 —54. Investigations of the properties of functionalized single-walled carbon nanotubes. H. F. Bettinger
12:00 —55. Interallylic bonding in the transition structures for
degenerate Cope rearrangements: Modification by substituents and by
strain, and the effects of changes in interallylic bonding on the
calculated barrier heights. W. T. Borden
Section A
Pennsylvania Convention Center -- 109B
1:30 — Introductory Remarks.
1:35 —56. Limitations of interactive drug design: Can de novo programs fill the gap? R. S. Bohacek
2:05 —57. Interactive rapid ligand prototyping: The MindRocket. C. M. W. Ho
2:35 —58. Improved methods for the de novo design of synthetically accessible ligands. A. P. Johnson, K. Boda, T. Lengyel, S. Weaver
3:05 — Intermission.
3:15 —59. Automated de novo design with LUDI, minimizer, QSAR, and scoring functions: Development and validation of AutoLudi. M. Lim-Wilby, J. Srinivasan, J. Koska, A. Krammer, C. M. Venkatachalam, M. Waldman
3:45 —60. Combinatorial computational ligand optimization. B. Tidor
4:15 — Concluding Remarks.
Section B
Pennsylvania Convention Center -- 104A&B
1:30 —113. Using decompositions in electronic structure methods to obtain reduced scaling. H. Koch, T. B. Pedersen, A. Sánchez de Merás
2:00 —62. Aromaticity beyond the organic chemistry domain. Z. Chen
2:30 —63. Diverting diradicals: From methylene to metal-dioxygen complexes. C. J. Cramer
3:00 —64. Coupled cluster calculations of optical rotation. T. D. Crawford
3:30 —65. Modeling mechanisms of hydron transfer in the condensed phase. N. A. Burton, R. Sharma, S. Nunez, G. Tresadern, I. H. Hillier
4:00 —66. Insights into mesoscale and electronic events during keV particle bombardment of solids. B. J. Garrison
4:30 —67. High-accuracy first-principles rovibrational spectroscopy. A. G. Császár
Section A
Pennsylvania Convention Center -- 202B8:00 - 10:00
68. Withdrawn.
69. Linking chemical and biological data using ChemCart and SRS Gateway for Oracle. M. Sud, A. Schafferhans, D. León, Y. Shimshock
70. Mechanistic insight from computer models of tyrosine kinase
mutations that cause ligand-independent activation of the receptor. M. Torrent, K. Rickert, B. Sheng-Pan, L. Sepp-Lorenzino
71. Computational identification of proteins for selectivity assays. S. Yoon, A. Smellie, D. S. Hartsough, A. Filikov
72. Physical basis for conformational energies in substituted ethanes. R. F. See
73. De novo computational method to increase ligand-receptor binding selectivity. D. L. Chen, G. E. Kellogg
74. Analysis of changes of protein fluctuation upon ligand
binding and incorporation of protein fluctuation into scoring function
development for structural-based drug design. C. Y. Yang, R. Wang, S. Wang
75. Calculations of hydration force. L. Tian, R. Zauhar
76. Can a QSAR model reliably predict a query compound’s activity? L. He, P. C. Jurs
77. Characterization of the ice/water interface with TIP4P-Ew water. T. J. Dick, J. D. Madura, P. Dalal
78. Redesigning interaction specificity of short peptide oligomerization domains. C. M. Taylor, M. H. Ali, B. Imperiali, A. E. Keating
79. Trajectory and energy perturbed multiple microcanonical
ensemble simulations for mapping potential energy landscapes and
conformations of polypeptides. Z. Huang, R. A. Wheeler
80. Improved workflow and results in the NMR lab: Integrated processing, prediction, searching, and data management. V. Rafalovsky, M. Scandone, D. Kernan
81. Modeling outer-sphere disorder in the symmetry breaking of PPV. L. A. Liu, D. Yaron
82. Structure and stability of lower fullerenes C38-C50 and nitrogen-substituted heterofullerenes. G. Sun
128. See subsequent listings.
Section A
Pennsylvania Convention Center -- 109B
9:00 — Introductory Remarks.
9:05 —83. BOMB for growing and scoring protein-ligand complexes. W. L. Jorgensen, J. Tirado-Rives
9:35 —84. CAPRI: Assessing protein docking algorithms in the blind structure prediction of protein-protein complexes. J. Janin
10:05 —85. Interdependence of docking performance and scoring accuracy in virtual screening. M. Kontoyianni, L. McClellan, G. Sokol
10:35 — Intermission.
10:45 —86. Virtual ligand screening by combined use of two grid-based docking methods, FLOG and ICM. V. N. Maiorov, R. P. Sheridan
11:15 —87. Critical assessment of docking programs and scoring functions. G. L. Warren,
W. Andrews III, A. M. Capelli, B. P. Clarke, J. M. LaLonde, M. H.
Lambert, M. Lindvall, N. Nevins, C. E. Peishoff, S. F. Semus, S.
Senger, G. Tedesco, I. D. Wall, J. M. Woolven, M. S. Head
11:45 —88. Improving the enrichment of high-throughput docking results using machine learning. A. E. Klon, M. Glick, J. W. Davies
12:15 — Concluding Remarks.
Section B
Pennsylvania Convention Center -- 104A&B
9:00 —89. Computational main group thermochemistry. D. A. Dixon, W. A. deJong, K. A. Peterson
9:30 —90. Remarkable structures and interaction potentials of clusters of molecular hydrogen and acetylenes. C. E. Dykstra
10:00 —91. Adventures in the land of triple bonds: The bonding situation in heavy-atom homologues of acetylene. G. Frenking
10:30 —92. Theoretical prediction of spectra. M. Frisch
11:00 —93. Reactions of ozone with acetylene: Density functional theory for concerted and stepwise mechanisms. J. D. Goddard, C. Weng, W. T. Chan
11:30 —94. Computational study of the mechanism and reactivity for the alkaline hydrolysis of N-phenylacetamides. B. Galabov, S. Ilieva, D. Cheshmedzhieva
Section C
Pennsylvania Convention Center -- 106A&B
9:00 — Introductory Remarks.
9:10 —95. Animations of intrinsic reaction coordinates for
pericyclic and pseudopericyclic reactions, including valley-ridge
inflection points. D. M. Birney, C. Zhou, S. V. Addepalli
9:40 —96. Conquer without dividing: Volume rendering of intact
molecular charge densities effectively illustrates key concepts in
bonding and reactivity. P. J. MacDougall, C. E. Henze
10:10 —97. Modeling, simulations and visualization in materials chemistry. T. Cagin
10:40 — Intermission.
11:00 —98. SymApps: A 3-D point group calculation and visualization tool. V. Rafalovsky, K. Nedwed, M. Scandone, G. M. Banik, D. Kernan
11:30 —99. Mol4D: Visualization and interactivity. J. H. Borkent
12:00 —100. VRML in the undergraduate curriculum. C. P. Calloway
Section A
Pennsylvania Convention Center -- 109B
1:30 — Introductory Remarks.
1:35 —101. PMF scoring revisited. I. A. Muegge
2:05 —102. Application of HINT interaction scores and
Hydropathic Intermolecular Field Analysis (HIFA) to the prediction of
ligand binding affinity. S. F. Semus, G. E. Kellogg
2:35 —103. How well can we score now and where do we go from
here: Comprehensive evaluation of 13 scoring functions on 800
protein-ligand complexes and development of new scoring functions. S. Wang, R. Wang, X. Fang, C. Y. Yang, Y. Lu
3:05 — Intermission.
3:15 —104. Improving accuracy in protein-ligand affinity calculations. M. K. Gilson, C. E. Chang, W. Chen
3:45 —105. Potential functions for virtual screening and ligand binding calculations: Some theoretical considerations. K. A. Sharp
4:15 —106. End-point free energy calculations: Synergy from continuum solvent and molecular dynamics methods. J. M. J. Swanson, J. A. McCammon
4:45 — Concluding Remarks.
Section B
Pennsylvania Convention Center -- 104A&B
1:30 —107. First principles predictions of the tertiary dtructures for membrane proteins. W. A. Goddard III
2:00 —108. Time-dependent density functional theory applied to carotenoids, chlorophylls and porphyrins. M. P. Head-Gordon
2:30 —109. Multireference spin-adapted variant of density functional theory. M. R. Hoffmann, Y. G. Khait
3:00 —110. Future prospects for Brillouin-Wigner-based quantum chemical methods. I. Hubac, S. Wilson, J. Pittner, P. Carsky
3:30 —111. Polarization consistent basis sets. F. Jensen
4:00 —112. Sigma bonds prevent short pi bonds. E. D. Jemmis, B. Pathak, H. F. Schaefer III, R. B. King
4:30 —61. Insights from momentum space. E. R. Davidson
Section C
Pennsylvania Convention Center -- 106A&B
1:30 — Introductory Remarks.
1:40 —114. Adding the third dimension to the chemistry lecture hall. J. J. Grabowski
2:10 —115. A novel mass spectrometry internet teaching tool. M. E. Bier, C. G. Yang, J. J. Grabowski
2:40 —116. VS-C: Cross-linked studies in chemistry. G. Fels
3:10 — Intermission.
3:30 —117. Web term papers: Learning structural biology through the creation of website content. W. H. Gallagher
4:00 —118. Animations of bio-organic reactions. P. B. Savage, S. A. Fleming
Section A
Pennsylvania Convention Center -- Hall D6:00 - 8:00
119. AEI: Knowledge-based potentials in drug design. B. N. Dominy
120. CoLiBRI: A novel method for the prediction of complementary
ligands based on receptor information and its application to database
screening. S. Oloff, S. Zhang, A. Tropsha
121. Parallel simulations of four-atom wavepacket dynamics. D. M. Medvedev, S. K. Gray, E. M. Goldfield
122. Computational design of protein complex with non-biological cofactor. W. Wang, F. Cochran, V. Nanda, S. Wu, M. J. Therien, W. F. DeGrado, J. G. Saven
123. Molecular dynamics simulation of E-coli dihydrofolate
reductase and its circular permuted variants: Relative stabilities in
experiment and simulations. Z. Hu, B. Ma, R. Nussinov, W. M. Southerland
124. Computational evaluation of stereoelectronic effects in fluorinated amines. J. J. Urban
125. Computational modeling studies of multi-targeted antifolates. A. J. Jackson, Z. Hu, W. M. Southerland
126. New algorithms for computational chemistry: Partial charges, resonance forms, symmetry, and conformational search. M. K. Gilson, M. J. Potter, W. Chen, H. S. R. Gilson, J. Huang
127. Computational studies of MALDI matrices interacting with tripeptides as a model of MALDI matrix-analyte interactions. F. H. Yassin, D. S. Marynick
128. Computational study of hyperthermophilic indole glycerol
phosphate synthase: Structural alterations at the active site with
temperature. D. Mazumder, T. C. Bruice
129. Computational study of the structure of di-lithium Phthalocyanine/Pyrite interface. Y. Zhang, L. G. Scanlon, P. B. Balbuena
130. Computational study on the role of bridging water molecules in the energetics of protein-ligand binding. M. Fornabaio, P. Cozzini, F. Spyrakis, A. Mozzarelli, D. J. Abraham, G. E. Kellogg
131. Computer simulation of acetone with a polarizable potential model. T. M. Chang, T. Lerro
132. Free energy calculations from non-equilibrium pulling simulations on a single peptide molecule. H. Xiong, H. P. Cheng, A. Roitberg
133. Computing the intrinsic conformational preferences of
substituted cyclohexanes and tetrahydropyrans: Some surprises and new
insights. A. K. Jones, G. S. Tschumper
134. Conformational analysis of piperazine and piperidine analogs of GBR12909: Effect of force field and solvent. D. Pandit, W. Roosma, M. Misra, K. M. Gilbert, D. Matecka, T. Prisinzano, K. C. Rice, C. A. Venanzi
135. Conformational study of polypeptides implicated in Alzheimer’s disease. T. H. Click, Z. Huang, R. A. Wheeler
136. Cytosine radicals and their respective anions: Molecular structure and electron affinities. D. J. Zhang
137. Defining privileged reagents using sub-similarity comparison: A method for reagent ranking. B. A. Tounge, C. H. Reynolds
138. Designing a combinatorial library of mutation-resistant HIV protease inhibitors. S. Chellappan, M. X. Fernandes, M. K. Gilson
139. Determination of cysteine pKas in a copper chaperone. R. R. Abd El-Rahman, J. D. Madura, C. T. Dameron
140. Determining partial atomic charges for fragments used in de novo drug design. J. L. Ludington, T. T. Fujimoto, F. P. Hollinger
141. Development of an effective strategy for lead docking. D. Cheney, L. Mueller, D. R. Langley
142. DFT, molecular dynamics, and free energy calculations on the multi-coordinate Cu(I)-binding protein Hah1. K. M. Merz Jr., B. T. Op't Holt
143. Effects of grid sizes on the calculation of solvation free energy in a quantum continuum solvation model. K. M. Merz Jr., N. Liao
144. Estimation of conformational entropy loss in protein-ligand binding process using 2-D and 3-D graph indices. X. Fang, R. Wang, S. Wang
145. Evaluation of semi-empirical methods for protein minimization and decoy discrimination. A. M. Wollacott, K. M. Merz Jr.
146. Human intestinal absorption (HIA) model using simple molecular descriptors. M. D'Souza, G. M. Banik
147. Fuzzy clustering as a means of classifying conformations of a flexible dopamine reuptake inhibitor. M. Misra, A. Banerjee, R. N. Davé, C. A. Venanzi
148. Homology modeling studies of Yersinia Kinase YpkA: Implications for structure-based drug design. X. Hu, G. Prehna, C. E. Stebbins
149. Ligand-based design of pyridinone derivatives with potential activity against mutant strains of HIV-1 reverse transcriptase. J. L. Medina-Franco, S. Rodríguez-Morales, A. Hernandez, C. Juárez-Gordiano, J. Jimenez-Barbero, R. Castillo
150. MD/NMR characterization of internal motions of peptide toxins. D. C. Chatfield, C. D'Cunha, A. Gairola, A. Augsten
151. Computational combinatorial protein design: Sequence search and statistical design. X. Yang, J. G. Saven
152. Filling the gap between conventional and “mean-field” molecular dynamics: Implementing the EXACT approximation. C. A. Hixson, J. Chen, Z. Huang, R. Wheeler
153. Fragmentation analysis of vibrational circular dichroism of polypeptides. J. H. Choi, M. Cho
154. Full quantum mechanical ab initio computation of protein-ligand interaction energy and QM map for protein-ligand binding. A. Gao, J. Z. H. Zhang
155. Important roles of crystallographic water molecules in
protein-ligand interaction: A comprehensive analysis of water molecules
observed in the X-ray crystal structures of protein-ligand complex. Y. Lu, R. Wang, C. Y. Yang, S. Wang
156. In silico screening for the hERG K+ ion channel affinity. M. Song, J. Bi, C. M. Breneman
157. Investigation of salt bridge strength in the Generalized Born water solvation model. R. Geney, C. L. Simmerling
158. Investigation of selenium-aromatic ring interaction in proteins. I. Hartman, R. Zauhar
159. MD simulation study of NMA-methanol system: Calculations of linear and nonlinear vibrational spectra. K. Kwac, M. Cho
160. Method for computing protein binding affinity. C. F. F. Karney, J. E. Ferrara, S. Brunner
161. Minimizing Lennard-Jones-dipole-dipole clusters: Improvements on the basin hopping strategy for parameter space searches. E. Curotto, C. Oppenheimer
162. Molecular dynamics simulations of the Glutamate Receptor GluR2 tetramer structure. K. Speranskiy, M. Kurnikova
163. Mutational studies of the Trp-cage mini-protein. M. M. Layten, B. A. Strockbine, N. H. Andersen, C. L. Simmerling
164. New scoring functions for discovery of lead peptides inhibitors for thrombin. C. Clement, M. Philipp
165. Non-Hamiltonian hybrid Monte Carlo algorithms for biophysical systems. M. Eleftheriou, G. Martyna
166. Novel conformational searching technique for low degree polymers. A. B. Silver, K. Sohlberg
167. Prediction of ligand binding modes and binding affinities of SAH/MTA nucleosidase inhibitors. J. K. Perry, V. A. Feher
168. Pyrolysis of styrene. J. Rienstra-Kiracofe, T. Pham, M. C. Lin
169. QSAR and molecular modeling studies of small molecule inhibitors of Plasminogen Activator Inhibitor-1. K. Y. Fan, H. Elokdah, D. L. Crandall, A. Aulabaugh, A. H. Katz
170. Quantum mechanical and docking studies of acetylcholinesterase inhibitors of the N-arylmaleimide type. J. L. Medina-Franco, R. T. Lino Joel, S. Rodríguez-Morales, R. Castillo, P. Melchor-Macias, J. Trujillo-Ferrara
171. 3D-QSAR comparative molecular field analysis on opioid receptor antagonists: Pooling data from different studies. Y. Peng, S. M. Keenan, Q. Zhang, V. Kholodovych, W. J. Welsh
172. Ab initio predictions of the heats of formation of nitroprismanes. T. P. Hamilton, O. Olubajo
173. Ab initio studies of the structure and bonding of sulfur and sulfoxonium ylides. J. M. Standard, B. A. Copack, T. K. Johnson, D. E. Przybyla, K. J. McDonald, R. J. Steidl, B. N. Ida
174. Ab initio studies on the structure and stability of the anion trimers of hydrogen fluoride, water and ammonia. X. Bai, P. Yang, R. E. Brown
175. Accurate calculation of aqueous host-guest binding affinities. W. Chen, C. E. Chang, M. K. Gilson
176. Analysis of protein-oligosaccharide docking interactions using principal component analysis. J. Leiss, P. Dalal, J. D. Madura
177. Characterization of unbound conformations of gp120 core domain. Y. Pan, B. Ma, R. Nussinov
178. Clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs. K. M. Gilbert, D. Matecka, T. Prisinzano, K. C. Rice, C. A. Venanzi
179. Collection of binding affinities for protein-ligand complexes with known 3-D structures: The PDBbind database. R. Wang, X. Fang, Y. Lu, C. Y. Yang, S. Wang
180. Component-based integration of chemistry and optimization software. J. P. Kenny, S. J. Benson, Y. Alexeev, J. Sarich, C. L. Janssen, L. Curfman McInnes, M. Krishnan, J. Nieplocha, E. R. Jurrus, C. A. Fahlstrom, T. L. Windus, D. E. Bernholdt
181. Computational approach to find selective Cox-2 inhibitors. M. Kumar, R. J. Zauhar
182. Intramolecular proton migration in fully deprotonated
myo-inositol 2-monophosphate and the formation of four-center hydrogen
bonds. P. Yang, X. Bai, R. E. Brown
183. Quantum chemical approach to understand the contribution of ligand functional groups to estrogen receptor-a/b selectivity. R. J. Unwalla, E. S. Manas
184. Refinement of ligand structure from a comparison of experimental and calculated chemical shift perturbations. B. Wang, K. Raha, K. M. Merz Jr
185. Selectivity between alkali-metal ions to 12-Crown-4 in MeOH: A Monte Carlo simulations study. H. S. Kim
186. Shape signatures and receptor based drug design. L. Tian, R. J. Zauhar
187. Simulation studies of helical m-phenylene ethynylene foldamers. O. S. Lee, J. G. Saven
188. The computational study of the deprotonation of cyclohexene oxide catalyzed by isopinocampheyl based chiral lithium amides. Y. Xiao, D. Jung, T. Gund, S. V. Malhotra
189. Theoretical study of the electron density distributions in a dipeptide molecule. K. M. Merz Jr., N. Yu
190. Towards novel therapeutics against HIV infection and drug resistance. Y. Che, G. R. Marshall, B. R. Brooks
191. Using similarity and classification methods to determine applicability of QSAR models to query set compounds. R. Guha, P. C. Jurs
192. Using walkers to find transition states from reactant and product minima. H. P. Hratchian, H. B. Schlegel
193. "Reverse-docking" as a computational tool for the study of asymmetric organocatalysis. D. J. Harriman, G. Deslongchamps
Section A
Pennsylvania Convention Center -- 104A&B
9:00 —194. Theoretical studies of atmospheric chemistry and developments in coupled-cluster theory. T. J. Lee
9:30 —195. Computational studies of molecular frame photoelectron angular distributions. R. R. Lucchese
10:00 —196. Modeling molecular interactions in MALDI mass spectrometry. D. S. Marynick
10:30 —197. Two face-to-face benzenes and o,o'-dibenzene:
Electronic states and photochemical interconversion. J. Tonne, M.
Schottelius, J. Chalupsky, Z. Havlas, H. Prinzbach, J. Michl
11:00 —198. Theoretical design of ion selective receptors. K. S. Kim
11:30 —199. Computational studies of the O-O bond activation and olefin epoxidation catalyzed by Mn-Salen complexes. K. Morokuma, I. V. Khavrutskii, R. R. Rahim, D. G. Musaev
Section B
Pennsylvania Convention Center -- 109B
8:30 —200. Development of an improved four-site water model for bio-molecular simulations: TIP4P-Ew. H. W. Horn, W. Swope, J. Pitera, J. D. Madura, T. J. Dick, G. L. B. Hura, T. Head-Gordon
8:50 —201. Studies of brine using TIP4P-Ew and DYNAMO. P. E. Krouskop, J. D. Madura
9:10 —202. Molecular level studies of water-mediated interactions between ions and their relevance to biomolecular interactions. S. Rajamani, T. Ghosh, S. Garde
9:30 —203. Reaction mechanism, free energy profiles and
structural changes along the reaction path of catalysis in the wild
type and two active site mutants of medium chain acyl-CoA
dehydrogenase. S. Bhattacharyay, M. T. Stankovich, J. Gao
9:50 —204. Novel "linear" Monte Carlo approach to free energy calculations. M. Clark, I. Shkurko, Q. Wang
10:10 —205. A structure and thermodynamic model of the binding
of botulinum neurotoxin Type A inhibitors computed by Monte Carlo
methods of docking and thermodynamic evaluation. L. Carlacci, M. Olson
10:30 —206. Liquid-liquid phase transitions in phosphorus: Insight from simulations. R. O. Jones, P. Ballone
10:50 —207. Systematic method for identifying reaction coordinates in complex systems. A. Ma, A. R. Dinner
11:10 —208. Directly calculated ligand binding free energies using Folding@Home. M. R. Shirts, G. Jayachandran, C. D. Snow, V. S. Pande
11:30 —209. Validation of a complete polarizable force field for
proteins by computing geometric and energetic properties of isolated
and solvated systems. G. A. Kaminski
11:50 —210. Ab initio and empirical model simulation studies of "neat" liquid water and of a solvated peptidic fragment in aqueous solution. Y. A. Mantz, B. Chen, H. Gerard, R. Iftimie, G. J. Martyna
Section A
Pennsylvania Convention Center -- 109B
1:30 —211. High performance computing in the Blue Gene project at IBM Research. W. Swope
2:05 —212. Folding@Home: Can a grid of 100,000 CPUs tackle fundamental barriers in molecular simulation? V. S. Pande
2:40 —213. Asymptotic improvement in the parallel evaluation of pairwise particle interactions. D. E. Shaw
3:15 — Intermission.
3:25 —214. Turbo-charged applications on ClearSpeed's streaming processors. S. McIntosh-Smith
4:00 —215. Evolution of the Locus "Titan" computing cluster. K. Milligan, M. Clark
4:35 —216. High performance computing at Novartis Institutes for Biomedical Research. D. Mikhailov
Section B
Pennsylvania Convention Center -- 104A&B
1:30 —217. Semiclassical correction to quantum energy levels. W. H. Miller, A. L. Kaledin, C. W. McCurdy
2:00 —218. Linear-scaling methods for large molecules: Development and application. C. Ochsenfeld
2:30 —219. Fritz Schaefer and the periodic table. R. M. Pitzer
3:00 —220. Thermochemistry of calcium-containing molecules: An examination of the performance of high-level theoretical procedures. L. Radom, M. B. Sullivan, N. L. Haworth, A. K. Wilson, L. A. Curtiss, J. M. Martin
3:30 —221. Resonant electron scattering by soft box CCSD(T) calculations. W. Meyer, D. Spelsberg
4:00 —222. Electroweak quantum chemical kinetics and molecular parity violation. M. Quack
4:30 —223. The ages of quantum chemistry. W. G. Richards
Section A
Pennsylvania Convention Center -- 109A
8:30 — Introductory Remarks.
8:35 —224. Kinematic view of loop closure. E. A. Coutsias, C. Seok
9:05 —250. Some uses of computer algebra in enzyme kinetics. N. Yildirim
9:35 —226. Enzyme kinetics using manifold theory. S. J. Fraser
10:05 — Intermission.
10:25 —228. Symbolic calculations in the theory of atoms. J. Javanainen
10:55 —225. Symbolic generation of perturbation equations for the vibrational-rotational analysis of potential energy surfaces. W. C. Ermler
11:25 —247. Symbolic computation in the determination of hyperspherical harmonics. A. Kuppermann
Section B
Pennsylvania Convention Center -- 104A&B
9:00 —229. Towards a universal potential for water. R. J. Saykally
9:30 —230. Towards an understanding of 3-D aromaticity. P. V. R. Schleyer, Z. Chen, R. B. King
10:00 —231. How to "Cope" with biradicals from enediynes and the like. P. R. Schreiner
10:30 —232. Recent progress in the development of exchange-correlation functionals. G. E. Scuseria
11:00 —233. Potential energies of weakly and strongly interacting systems: From pi-stacking to bond-breaking. C. D. Sherrill
11:30 —234. Thermodynamic and kinetic simulations of protein folding at IBM Research. W. Swope
Section C
Pennsylvania Convention Center -- 103C
8:20 —235. Quantum mechanical studies of HIV-1 protease inhibitors and drug design based on full ab initio MFCC computation. D. Zhang, J. Z. H. Zhang
8:40 —236. PREDICT modeling and in silico screening for GPCR: From amino acid sequence to the clinic. S. Shacham, Y. Marantz, S. Noiman, O. M. Becker, M. G. Kauffman
9:00 —237. QMQSAR: A semi-empirical (PM3) field-based QSAR program. S. Dixon, K. M. Merz Jr., G. Lauri, J. Ianni, M. C. Kozlowski
9:20 —238. Computational investigations on novel catalytic antibodies: Aldolase and anti-cocaine. Y. Hu, A. Olson
9:40 —239. Importance of electric charges in molecular docking: QM/MM approach. A. E. Cho, V. Guallar, B. J. Berne, R. A. Friesner
10:00 —240. Computer-aided design of novel natural-product-based matrix metalloproteinase-3 inhibitors. E. A. Amin, W. J. Welsh
10:20 —241. High quality homology models for structure-based drug design: A comparative study. A. Nayeem, D. Sitkoff, S. Krystek Jr.
10:40 —242. GQSAR: A new ab intio/DFT 3-D-QSAR program. J. Ianni, M. Kozlowski
11:00 —243. Graph isomorphisms for computer-aided drug discovery. N. T. Southall, T. Nguyen, D. Ajay
11:20 —244. Conformational consensus as a method to distinguish agonists from antagonists II: Identification of selective conformations. G. J. Tawa, A. H. Katz, J. C. Alvarez
11:40 —245. Lead docking protocol featuring improved sampling and scoring. L. Mueller, D. R. Langley, D. L. Cheney
246. Withdrawn.
Section A
Pennsylvania Convention Center -- 109B
248. Withdrawn.
1:15 —249. Symbolic computation in coupled cluster theory. P. Piecuch
1:45 —227. Conventional and unconventional symbolic computation in chemistry. F. E. Harris
2:15 — Intermission.
2:35 — Panel Discussion.
4:35 — Concluding Remarks.
Section B
Pennsylvania Convention Center -- 104A&B
1:30 —251. Computational strategies for high-accuracy computations of hydrogen bonding and π - π stacking prototypes. G. S. Tschumper
2:00 —252. Conical intersections are generalized lines not isolated points. D. R. Yarkony
2:30 —253. High accuracy theoretical pKa calculations. B. F. Yates, A. M. Magill
3:00 —254. Three- vs. four-coordinate phosphorus: More reasons for tight d functions. S. S. Wesolowski
3:30 —255. Ab initio vibration-rotation spectroscopy. W. Thiel
4:00 —256. Modeling of the CVD of 13-15 composites: From donor-acceptor complexes to rings and clusters. A. Y. Timoshkin
4:30 — Concluding Remarks. Henry F. Schaefer III.