| BUSINESS MEETING: Sat |
Section A
Unknown Site
8:30 1. Target validation and drug discovery: an overview. D.
Kallick
9:05 2. Development and Application of a Technology
Platform for High Throughput Structure-Guided Drug Discovery. S. W.
Kaldor
9:40 3. Discovery informatics: Integrating genomics
and proteomics for drug discovery. M. D. Adams
10:15
Intermission.
10:25 4. Genomics-driven structure-based drug
discovery. T. Klingler, K. Lind, V. Tsui
11:00 5. Kinases
versus protein-protein interactions: different opportunities and challenges in
drug discovery. C. Garcia-Echeverria
Section B
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8:10 Introductory Remarks.
8:30 6. All element
augmentation to MM3. G. D. Purvis III
9:00 7. Development
of a more accurate AMBER united-atom force field for protein folding and
large-scale biomolecular simulations. R. Luo, J. Wang, P. A.
Kollman
9:30 8. Performance of empirical force fields in the
modeling of nucleic acid structure, dynamics and interactions T. E. Cheatham
III
10:10 Intermission.
10:30 9. OPLS_2002:
A new version of the OPLS-AA force field. W. Damm, T. A. Halgren, R. B.
Murphy, A. M. Smondyrev, R. A. Friesner, W. L. Jorgensen
11:10 10. CHARMM Biomolecular Force Field: Recent developments and future
directions. A. D. MacKerell Jr.
Section C
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8:00 Introductory Remarks, Bruce Garrett
8:05 11.
Quantum Molecular Dynamics in Liquids. B. J. Berne
8:45 12. Solvation of the excess proton in complex environments. G. A.
Voth
9:25 13. Theoretical studies of proton-coupled electron
transfer reactions in solution. S. Hammes-Schiffer
10:05
Intermission.
10:15 14. Modeling non-adiabatic excited
state charge transfer to solvent dynamics. D. F. Coker, N.
Yu
10:55 15. Simulation of quantum molecular processes using
entangled classical trajectory ensembles. C. C. Martens
11:35 16. Inversion and Ill-poised Problem in Computing Nonadiabatic Electron
Transfer Rate Constants. J. Liao, G. A. Voth
Section A
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1:30 17. Industrialization of drug discovery. J. S.
Handen
2:05 18. Finding important disease genes using mass
spectrometry. C. R. Cantor
2:40 19. Using mammalian
genetics to validate drug discovery targets for small molecule intervention.
A. Main
3:15 Intermission.
3:25 20. The
personalized medicine strategy in drug discovery. G. S.
Ginsburg
4:00 21. A comprehensive systems biology approach
to identify key novel targets for drug development. R. D. Klein
Section B
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1:30 Introductory Remarks.
1:40 22. Chemical
potential equalization: A many-body force field for molecular simulations. D.
M. York
2:20 23. New electrostatic and valence aspects of a
spectroscopically determined force field (SDFF) for the peptide group. K.
Palmo, B. Mannfors, N. G. Mirkin, S. Krimm
3:00
Intermission.
3:10 24. TINKER polarizable atomic multipole
force field for proteins. P. Ren, J. W. Ponder
3:50 25.
Polarizable force fields: new physics, new questions, new problems C. L.
Brooks III
4:30 26. Development of a polarizable force field
for proteins and pharmaceutical compounds. R. A. Friesner, G. Kaminski,
H. A. Stern, J. Maple
Section C
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1:30 27. The role of solvation dynamics in hydrophobic collapse.
D. Chandler
2:10 28. Protein solvation in membranes and
at water-membrane interfaces. A. Pohorille, C. Chipot, M. A.
Wilson
2:50 29. Hydrophobic and hydrophilic behavior in bulk
water and confined systems. J. C. Rasaiah
3:30
Intermission.
3:45 30. Synchrotron experiments and theory:
pure water as a function of temperature. T. Head-Gordon, G. L. B. Hura,
D. Russo, R. M. Glaeser
4:25 31. Issues of solvation in drug
design. T. R. Stouch
5:05 32. Probing quantum solvation
through infrared spectroscopy: Dopant-induced infrared activity in solid
hydrogen. R. J. Hinde
Section D
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1:00 Introductory Remarks.
1:10 33. Nanowires as
building blocks for nanoscale science and technology. C. M.
Lieber
1:55 34. An integrated systems-oriented approach to
molecular electronics. J. F. Stoddart
2:40 35. Molecular
quantum-dot cellular automata. C. S. Lent, B. Isaksen, M.
Lieberman
3:05 Intermission.
3:20 36. Molecules
and supramolecular arrays for quantum-dot cellular automata. M.
Lieberman, S. Chellamma, Y. Wang, Q. Hang, G. Bernstein, C. S.
Lent
3:45 37. Structure analysis of discotic liquid crystals
containing 1,3,5-tri-substituted benzene core and conjugated oxadiazole arms
using XRD and computer simulation methods C. R. Park, S. H.
Gihm
4:10 38. Silicon segregation from SiO_(2-x) sub-oxides:
Dynamical Monte Carlo study. P. Ballone, R. O. Jones
4:35 39. Molecular toolbox: a physical organic chemistry approach to molecular
electronics. J. Hu, C. Khemtong, Y. Liu
Section A
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8:30 40. Organizing research by gene family. M.
Murcko
9:05 41. Identifying function first toward lead
discovery in the post-genomic era. S. M. Baxter, P. Domaille, S. Betz, S.
Knutson, K. Burdick, B. Hoffman, J. Fetrow
9:40 42. Drug
Discovery on a Proteomic Scale. M. V. Milburn
10:15
Intermission.
10:25 43. Homology modelling and simulation
studies on the orphan nuclear receptor err-g. W.
Cornell, K. Nam, R. Wolf, P. Marshall
11:00 44. Patenting
3-D structures. A. A. Russo
Section B
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8:00 Introductory Remarks.
8:10 45. Extending the
MM3 force field for application to the structure-based design of metal ion
hosts. B. P. Hay
8:50 46. Interplay of bonding theory and
force fields for organotransition metal complexes. C. R.
Landis
9:30 Intermission.
9:50 47. De Novo
structural prediction of transition metal complexes. T. Cundari, C.
Buda
10:30 48. Selectivity in the addition of dialkyl zinc to
aldehydes from Q2MM force field modeling. P. Norrby, T. Rasmussen, M. B.
Gillies
11:10 49. Importance of conformational searching:
understanding prochiral olefin binding to chiral cyclopentadienyl complexes of
rhenium and the case of the missing conformers. D. White, A. M.
Gillespie, G. R. Morello, M. A. Freeze
Section C
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8:00 50. The coupling of solvent and electronic dynamics in excited
state relaxation. P. J. Rossky
8:40 51. Dynamics in
liquid water: Computational approaches to calculating ultrafast infrared
spectroscopy observables. J. L. Skinner
9:20 52.
Solvation dynamics in multicomponent systems and supercritical fluids. B. M.
Ladanyi
10:00 Intermission.
10:15 53. How
the vibrational modes of a polyatomic molecule see a solvent. R. M.
Stratt, Y. Deng
10:55 54. Energy relaxation in liquids: HDO
in D2O. P. A. Bopp, S. J. -. Cousineau
11:35 55. A new theory for solution-phase vibrational energy relaxation. E.
Geva, Q. Shi
Section D
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8:30 Introductory Remarks.
8:35 56. Virtual
screening with topomeric CoMFA. R. D. Cramer
9:15 57.
Building QSAR models from large screening sets. P. Blower, K. Cross, M.
Fligner, R. Khramets, G. Myatt, J. Verducci
9:45 58. 4D-QSAR and
CoMFA of ligand actuators for the ecdysone receptor-mediated gene transcription
system. R. E. Hormann, O. Chortyk, D. E. Cress, A. J. Hopfinger, C. S.
Thompson
10:15 Intermission.
10:30 59. Motion
of molecular probes in the functional sites of proteins. T. Kortvelyesi,
S. Dennis, S. Vajda
11:00 60. Optimized lead discovery combining
ligand-based and structure-based methods. W. Mydlowec, G. Lanza, J.
Yu
11:30 61. Ligand-based lead discovery and applications to
"scaffold hopping". G. Lanza, J. Yu, W. Mydlowec
Section A
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1:30 62. Mining the NCI's tumor screening and genomic databases:
Relating molecular targets to candidate ligands. D. G. Covell, A. A.
Rabow, A. Wallqvist, R. H. Shoemaker
2:05 63. Novel
bioinformatics techniques in functional genomics. A. J.
Butte
2:40 64. Model-centric data integration and the
development of genome-scale models of metabolism. C. H.
Schilling
3:15 Intermission.
3:25 65.
Molecular Profiling in Drug Discovery and Development. R. G.
Ulrich
4:00 66. Expanding predictive toxicology applications
using toxicogenomics. D. L. Mendrick
Section B
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1:30 Introductory Remarks.
1:40 67. Ground state
near attack conformers (NACs) and transition states in enzyme reaction. T. C.
Bruice
2:20 68. Combining quantum mechanics, molecular
mechanics, and molecular dynamics to model enzyme and antibody catalysis K.
N. Houk
3:00 69. Development and applications of transition
state force fields. M. B. Gillies, P. Norrby
3:40
Intermission.
3:50 70. Empirical valence bond strategies
for phosphoryl and nucleotidyl transfer reactions. J. Florian, A. Shurki,
A. Warshel
4:30 71. Multi-configuration molecular mechanics.
D. G. Truhlar, T. V. Albu
Section C
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1:30 72. Forward-Backward Semiclassical Dynamics. N.
Makri
2:10 73. Desolvation effects upon ion transport
through narrow protein channels. R. D. Coalson, A. Mamonov, M. Kurnikova,
A. Nitzan
2:50 74. Molecular modeling of proton conduction in
polymer electrolyte membranes of nafion¨ type. L. R. Pratt, M. Eikerling,
S. J. Paddison, T. A. Zawodzinski
3:30 Intermission.
3:45 75. Ensemble-averaged variational transition state theory
with optimized multidimensional tunneling. D. G. Truhlar, J. Gao, C.
Alhambra, J. Corchado, M. Garcia-Viloca, M. L. S‡nchez, L. D. Kesavan, T.
Poulsen, J. Villa
4:25 76. Perturbed Hard-Body Fluid Theoretical
Analysis of Solvent Effects on Chemical Reactions. D. Ben-Amotz, A. Gift,
B. L. McClain
5:05 77. Ab initio molecular dynamics
investigation of proton transport in liquid methanol. J. A. Morrone, M.
E. Tuckerman
Section D
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1:30 78. QSAR prediction of drug toxicity. J. C.
Dearden
2:15 79. ADME profiling in drug discovery:
Comparison of rule-based computational alerts to mechanism-based simulation.
M. B. Bolger, R. Fraczkiewicz, B. Steere
2:45 80.
Classification of cytogenetic toxicity of organic compounds from molecular
structure. N. R. McElroy, P. C. Jurs
3:15 Intermission.
3:30 81. QSAR modeling of b-lactam binding to serum protein.
L. B. Kier, L. H. Hall, L. M. Hall
4:00 82. Property
modeling independent of 3D information: Blood-Brain barrier penetration and fish
toxicity. L. H. Hall, L. B. Kier
4:30 83. Analysis of
structure-activity relationships of P-glycoprotein mediators for development of
a new P-glycoprotein inhibitor: Pyronaridine. C. Yang, J. Qi, S. Wang, H.
Peng
7:00 - 9:00
132, 142-144, 146, 149, 155, 157, 162, 165, 182, 186, 190. See subsequent listings.
Section A
Unknown Site
8:30 84. Structural proteomics of eukaryotic protein families. J.
F. Hunt
9:05 85. Function based profiling of proteases.
J. L. Harris, N. Winssinger, R. Damoiseaux, B. J. Backes
9:40 86. From proteins to drugs - identification of regions of proteins involved
in intramolecular interactions. M. Clark, S. Brunner
10:15
Intermission.
10:25 87. Automatic identification of protein
functional sites using BioDOCK. S. K. Schlyer, D. C. Roe, M. M.
Young
11:00 88. Binding mode of VEGF receptor tyrosine
kinase KDR (VEGFR-2) inhibitors. G. McGaughey, M. Bilodeau, K. Coll, J.
Gibbs, G. Hartman, W. Huckle, R. Hungate, A. Johnson, R. Kendall, T. Koester, N.
Kohl, X. Mao, R. McFall, B. Pan, K. Rickert, L. Rodman, R. Rutledge, K.
Thomas
Section B
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8:30 Introductory Remarks.
8:45 89. Accurate and
efficient many-body potential for hydrogen bonding - application to water. P.
Ballone, J. Akola, R. O. Jones
9:15 90. Developing
transferable force fields for phase equilibrium calculations. J. I.
Siepmann, C. D. Wick, J. M. Stubbs, N. Zhuravlev, L. Zhang, J. Lee, X. Zhao,
M. G. Martin, B. Chen, J. J. Potoff
9:45 Intermission.
10:10 91. Hardware accelerator for molecular force fields.
F. H. Bennett III, W. Mydlowec
10:40 92. Force field
dependence of NMR-based, restrained molecular dynamics DNA structure
calculations including an analysis of the influence of residual dipolar coupling
restraints M. A. Kennedy, K. McAteer
11:10 93. A Critique
of GBSA. A. Nicholls, A. Grant
Section C
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8:30 Introductory Remarks.
8:40 94. Protein
modeling in education. G. D. Purvis III
9:10 95. LUCID:
Web-based team learning and real-time multilevel assessment for introductory
chemistry. T. A. Wolfskill, D. Hanson
9:40 96. Impact of
adding interactive problem-analysis help to web-based homework assignments.
K. I. Barnhard, J. W. Moore
10:10 Intermission.
10:20 97. The Use of Technology to Facilitate Interactive
Learning of Chemistry at the United States Military Academy. A. W. Fountain
III
10:50 98. Examples of computer use in undergraduate
physical chemistry. D. G. Miles Jr.
11:20 99. Student
manipulation of microscopic reaction trajectories. A. Grushow
Section D
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8:30 Introductory Remarks.
8:40 100. Predictive
ADME: Why models fail. T. R. Stouch, S. Johnson
9:20 101.
On the detection of multiple binding modes of ligands to proteins, from
biological, structural, and modelling data P. Lewi, M. de Jonge, F.
Daeyaert, L. Koymans, M. Vinkers, J. Heeres, P. A. J. Janssen, E. Arnold, K.
Das, A. D. Clark Jr., S. H. Hughes, P. L. Boyer, M. -. de BŽthune, R. Pauwels,
K. Andries
10:00 Intermission.
10:15 102.
Theory and practice of safe QSAR. A. Tropsha, Y. Xiao, M. Shen, S. Oloff,
A. Golbraikh
10:45 103. Effect of training and test set
diversity on PLS statistics. R. D. Clark
11:15 104. Are
topological parameters "fundamental properties"? Evidence from the solubility of
gases in liquids M. Charton
Section A
Unknown Site
1:30 Introductory Remarks.
1:40 105. Geminals-based
model chemistry. V. A. Rassolov
2:10 106. A
linear-scaling quantum chemistry method for ground and excited states:
Localized-density-matrix method. G. Chen
2:40 107. Monte
Carlo simulation of proteins through a random walk in energy space. N.
Rathore, J. J. de Pablo
3:10 Intermission.
3:30 108. Direct calculation of molecular free energies. C. Chang, M. K.
Gilson
4:00 109. High throughput prediction of passive ADME
properties from fragments. T. I. Oprea, M. Baroni, I. Zamora, G.
Cruciani
4:30 110. Priviledged substructure searching for
focused set design. C. Cleva, D. Domine, C. Merlot, J. Bunn, E. Sebille,
W. Sauer, D. Church
5:00 Tally of Judges' Reports, Remarks about
COMP, and Award Presentation
Section B
Unknown Site
1:30 Introductory Remarks.
1:40 111. Theory and
experiment: molecular modeling exercises designed to increase conceptual
understanding. J. B. Foresman
2:10 112. Using web-based
homework and quizzes to redesign a general chemistry course. J. W. Moore,
K. I. Barnhard, R. S. Cole, J. B. Todd
2:40 113. Beyond quantum
chemistry: A course in mathematical modeling for chemists. M. M.
Francl
3:10 Intermission.
3:20 114.
Essential role of informatics in computational biochemistry/chemistry
curriculum. M. Shibata, S. S. Haque
3:50 115. A rigorous
senior-level modeling course: How much is too much for three credits? T. J.
Zielinski
4:20 116. What does the evaluation of physical
chemistry on-line projects tell us about implementation and use of
computer-supported instruction and learning? M. Towns, L. Slocum, R. S.
Cole, T. J. Zielinski
Section C
Unknown Site
1:30 117. Properties of water in micellar solutions:Results from
computer simulations. M. L. Berkowitz, S. Senapati, C. D. Bruce, L.
Perera
2:10 118. Simulations of Selectivity and Permeation in
Channels. D. Henderson, D. Boda, D. Busath
2:50 119.
Energy Transfer and Chemical Reaction Dynamics at Interfaces. W. L.
Hase
3:30 Intermission.
3:45 120. Solvation
and ionization stages of HCl adsorbate on ice nanocrystals. V. Buch, J.
P. Devlin, J. Sadlej, N. Uras-Aytemiz
4:25 121. An inhomogeneous
model of protein dielectric properties:Intrinsic polarizabilities of amino
acids. X. Song
4:45 122. Vibrational relaxation at liquid
interfaces. I. Benjamin
Section D
Unknown Site
1:30 123. QSAR studies for Estrogen receptor PET tracers. D. E.
Reichert, P. Wolohan
2:15 124. Chain melting temperature
estimation for phosphatidylcholines by quantum mechanically derived QSPR. A. J.
Holder, D. A. White, D. M. Yourtee, A. G. Glaros, R. Smith
2:45 125. Classification of HIV Protease inhibitors and prediction of their
antiviral potency from molecular structure. S. J. Patankar, P. C.
Jurs
3:15 Intermission.
3:30 126. Development
of QSAR and classification models to predict inhibition and selectivity of DHFR
inhibitors. B. E. Mattioni, P. C. Jurs
4:00 127. New
developments in PEST shape/property hybrid descriptors. C. M. Breneman,
N. Sukumar, C. M. Sundling, L. Shen, B. Jiang, B. Katt, M. Song, H. Zhang, M. J.
Embrechts
7:00 - 9:00
128. Systematic comparison of density functionals. X. Wang, A. Lowe,
Q. Wang, J. Briggle, A. K. Wilson
129. Ab initio studies of
the structure and bonding of sulfur ylides. J. M. Standard, T. K.
Johnson, B. A. Copack
130. 2-Aminoethoxydiphenyl borate, a
computational and experimental study M. A. Collins, T. A.
Holme
131. Mechanistic Details of Aldehyde Dehydrogenase Chemistry
from MM and QM/MM Simulations. T. Wymore, M. J. Field, D. Deerfield II,
H. B. Nicholas Jr., J. Hempel
132. Models of bis(oxazoline)-Cu(II)
complexes upon Diels-Alder reactions. J. DeChancie, O. Acevedo, J. D.
Evanseck
133. Reactions of metal atoms with carbonyl compounds:
Comparisons of theory and experiment. C. A. Bayse
134.
Ab Initio Direct Dynamics Simulation of CH3CH2F
¨ CH2=CH2 + HF Unimolecular
Dissociation: A Case Study to Compare Wigner and Quasicalssical Initial
Condition Sampling Methods. L. Sun, W. L. Hase
135. Direct
Dynamics Simulation of Protonated Diglycine Surface Induced Dissociation. Y.
Wang, W. L. Hase
136. Quantum-mechanical reaction rate
and vibrational energy relaxation rate constants from Centroid Molecular
Dynamics (CMD) simulations. Q. Shi, E. Geva
137.
Theoretical Studies of the Collision-Induced Dissociation of Metal Clusters.
P. LarrŽgaray, G. Peslherbe
138. Study of the structural
and dynamical properties of a biomimetic compound of diiron proteins via ab
initio and hybrid (QM/MM) molecular dynamics simulations. A. Magistrato,
U. Ršthlisberger, M. L. Klein
139. Bridged binuclear metal motif:
General features through simple Mg(II) and Zn(II) models. P. Munih, M.
Karplus, G. A. Petsko, D. Ringe
140. Molecular dynamics
simulations of a small protein in aqueous solvent using a fluctuating charge
forcefield. S. A. Patel, A. D. MacKerell Jr., C. L. Brooks
III
141. Molecular modeling of NAALADase/PMSA inhibitors.
D. Wang, O. Wiest, P. Helquist, M. Miller, M.
Tenniswood
142. GTP-binding and association of the Escherichia
coli signal recognition particle protein, Ffh, and its receptor, FtsY K.
M. Elkins, I. Sinning, R. C. Wade
143. Impact of lipid
structure and dynamics upon laser-induced fluorescence detection and separation.
A. Loccisano, J. D. Evanseck, M. Johnson
144. Structure
Based InhA Inhibitor Design Aided by OWFEG. G. Cui, D. Marin, P. Tonge,
C. Simmerling
145. The Determination of pKa's in Proteins. R. R.
Abd El-Rahman, J. D. Madura, C. T. Dameron
146. Probing the
link between catalytic rate and enzyme dynamics in the hydride transfer reaction
catalyzed by dihydrofolate reductase. I. F. Thorpe, C. L. Brooks
III
147. Finding base-pairs and helical regions in nucleic acid
structures. X. Lu, Y. Xin, W. K. Olson
148. Locating
the experimental structure of a nonhelical nucleic acid by combined locally
enhanced sampling and continuum electrostatics approach. X. Cheng, C.
Simmerling
149. Molecular dynamics simulation and free energy
analysis of polycyclic aromatic carcinogen-damaged DNA: Accurate representation
and new insights. S. Yan, M. Wu, N. E. Geacintov, S.
Broyde
150. Probing the mechanism of base flipping in DNA via
Potential of Mean Force calculations. N. Huang, N. K. Banavali, A. D.
MacKerell Jr.
151. Molecular dynamics simulations on the wild-type
human transthyretin and its variants. M. Yang, M. Lei, S.
Huo
152. Folding and refolding simulations of beta-hairpin
peptides in explicit solvent. H. Lei, P. E. Smith
153.
Application of simplicial neighborhood analysis of protein packing (SNAPP) to
binding proteins that undergo conformational change. D. B. Sherman, S.
Zhang, J. B. Pitner, A. Tropsha
154. A comparison of the Low Mode
and Monte Carlo conformational search methods. J. Pratt, C.
Parish
155. Comparing the conformational behavior of a series of
enantiomeric cyclic urea HIV-1 inhibitors. K. Schram, C.
Parish
156. Molecular modeling and conformational analysis of
polyazamacrolides. E. Smith, C. Parish
157. Comparing the
conformational flexibility of HIV-1 inhibitors. J. James, J. Pratt, K.
Schram, C. Parish
158. Automating the prediction of enzyme active
sites from structure alone in THEMATICS. R. P. Futrelle, R. J. Williams, W.
Tong, M. J. Ondrechen
159. Computational approaches for
predicting androgenic activity: homology modeling of the androgen receptor and
calculation of ligand binding affinities. A. Ni, S. Yu, R. K. DeLisle, W.
J. Welsh
160. Computational studies of raloxifene (Evista)
derivatives: 3D-QSAR/CoMFA models and binding energy calculation as a guide for
selective estrogen receptor modulators (SERMs). S. Yu, D. Derington, W.
Welsh
161. Computational study of cyclooxygenase inhibitors:
3D-QSAR/CoMFA models for COX-1 and COX-2. A. Ni, S. Yu, W.
Welsh
162. Docking of novel Melatonin ligands to homology models
of MT1 and MT2. E. X. Esposito, T. Wymore, P. Li,
J. D. Madura
163. Docking studies of a conformationally rigidified
analog of L-778,123, a potent Farnesyltransferase inhibitor: Investigation of
the effect of charge models on docking results I. Merino, Y.
Pang
164. PfPK5 a novel kinase target for antimalarial drugs:
protein homology modeling and in silico design of potent and selective
inhibitors. S. Keenan, W. Welsh
165. Predicting biological
activity of a set of compounds using machine learning algorithms. K. Nam,
C. Honer, C. Schumacher, C. Berry, P. Marshall, W. Cornell
166.
Rational computer-aided design of opioid analogues: 3D-QSAsR models for d, m, and k
opioid receptors S. Yu, A. Nair, J. Duchek, W. Welsh
167.
Rational design of beta-peptide inhibitors of p53-mdm2 interaction. H.
Zhong, L. M. Sandvoss, H. A. Carlson
168. A theoretical
investigation on the binding of HLA-A2-peptide complexes. T. G. Kucukkal,
E. X. Esposito, J. R. Kovacs, S. P. Chamarthy, W. S. Meng, J. D.
Evanseck
169. The docking and binding affinity calculations of
TIMBO analogue inhibitors in HIV-1 RT. Z. Zhou, J. D.
Madura
170. Use of Dock and PB in Reproducing the Binding Mode and
Predicting the Binding Free Energies of Non-nucleoside Inhibitors to HIV-1
Reverse Transcriptase. Z. Zhou, J. Madura
171. Unusual
binding of oligosaccharides in the active site cleft of family 18 chitinases.
P. Dalal, N. N. Aronson Jr., M. F. Alexyev, L. Amable, B. A. Halloran, P.
VanRoey, J. D. Madura
172. Novel methodologies in training set
selection for pharmacophore modeling: a pharmacophore model of p38 MAP kinase
inhibitors. S. Varma, R. Hoffmann
173. QSAR study of
genotoxicity and cytotoxicity of a series of naphthoquinones. J. L. Roberts,
J. C. Dearden, R. F. Bilton
174. Consideration of molecular
weight during compound selection in virtual database screening. Y. Pan,
A. D. MacKerell Jr.
175. OEChem. M. T. Stahl, A. G.
Skillman, R. Sayle
176. PyOEChem. M. T. Stahl, R. A. Sayle,
A. G. Skillman
177. Ptree-Based Approach to Mining Gene Expression
Data. F. pan Sr., X. Hu, W. William
178. Application of
fuzzy methods to the analysis of conformational spaces for organometallic
moieties. D. White, M. A. Freeze II, A. M. Gillespie, G. R.
Morello
179. Theoretical Study on the Gas-Chromatographic Elution
of Compounds on Columns with Different Polarity. T. Kortvelyesi, K.
Heberger, K. Nagy, M. Gorgenyi
180. CoMFA study of protonated
methylphenidate phenyl-substituted analogs. K. M. Gilbert, M. Misra, R.
A. Buono, C. A. Venanzi, M. M. Schweri, Q. Shi, H. M. Deutsch
181.
2-Dimensional conformationally sampled pharmacophore: A novel aproach to ligand
based pharmacophore development applied to d opioid
ligands. D. Bernard, A. Coop, A. D. MacKerell Jr.
182. New
quantum indices for macromolecular characterization. J. Khandogin, D.
York
183. Novel QSAR/QSPR methods for predicting the acute
toxicity of organic compounds. B. Jiang, C. M. Breneman, N. Sukumar, M.
J. Embrechts
184. Novel Use of Self-Organizing Feature Maps in
QSAR Studies. A. J. Clauset, W. S. Caldwell, J. D.
Schmitt
185. Pharmacophore identification and bioactivity
prediction based on the TAE electronic conformation method. M. Song, C.
M. Breneman, D. Zhuang, N. Sukumar
186. Prediction of glass
transition temperatures for polymers using the TAE/RECON method. Q. Luo,
N. Sukumar, C. M. Breneman, K. Bennett, M. J. Embrechts
187. QSAR
analysis of fungal N-myristoyltransferase inhibitors: Correlation between enzyme
inhibitory activity and interaction energies calculated by ab-initio molecular
orbital methods. K. Morikami, K. Hasegawa, S. Sogabe, Y. Shiratori, H.
Ebiike, K. Kawasaki, M. Masubuchi, T. Ohtsuka, K. Sakata, T. Fujii, Y. Aoki, N.
Shimma
188. TACS (Targacept Active Conformation Search): a New
Method for Predicting the Conformation of a Ligand Bound to its Protein Target.
J. Klucik, A. J. Clauset, P. S. Hammond, R. Harris, W. S. Caldwell, J. D.
Schmitt
189. Virtual high throughput screening of ion receptors.
T. K. Firman, B. P. Hay
190. Application of Theoretical
Linear Solvation Energy Relationships to Human Intestinal Absorption. D. R.
Rakijian, T. Duong, G. R. Famini, L. Wilson, M.
Payne
191. ªgLatent membrane permeabilityªh concept: QSAR
analysis of inter- and intra-laboratorically variable Caco-2 cell permeability.
F. Yamashita, S. Fujiwara, M. Hashida
192. Diffusive step
method for determining the fully anisotropic rotational diffusion tensors of
spin labels tethered to macromolecules. D. E. Budil, M. Micalizzi, L.
Jiang, E. Darien, P. M. Gannett
193. Quantum chemical calculations
of cadmium chemical shielding tensors in biologically relevant molecules. S.
S. Kidambi, A. Ramamoorthy
194. Molecular dynamics studies on
polymer cold crystallization from an oriented amorphous state. A. Koyama,
T. Yamamoto, K. Fukao, Y. Miyamoto
195. Multicanonical Monte Carlo
study of liquid-solid phase transition of argon. C. Muguruma, Y. Okamoto,
M. Mikami
196. Large-scale simulations of clay-polymer
nanocomposites using grand-canonical Monte Carlo and molecular dynamics
approaches. P. Boulet, S. Stackhouse, P. V. Coveney
197. An
efficient method for the direct calculation of the excess entropy using the
average of acceptance ratios. S. D. Hong, D.
Jang
198. A new hydrogen bonding paradigm: Differing
electrical interactions in C-HáááO and O-HáááO hydrogen bonds of formic acid.
W. Qian, S. Krimm
199. Theoretical Applications of Chemical
and Physical CO2 Sequestration. T. J. Dick, P. Dalal, J. D.
Madura
200. Elucidating the form of MgO-CH4 and
CH4-CH4 interactions in the adsorbed phase. P. J.
Stimac, R. J. Hinde, J. Z. Larese
201. Quantum chemical
studies of the solvent decomposition in lithium-ion battery electrolyte. Y.
Han, S. U. Lee, J. Jung
202. Interpreting brown dwarf
atmospheric absorption spectra: The Na -- He dimer. T. C. Lillestolen, R.
J. Hinde
203. Monte Carlo simulations for isotopic substutions in
neutron studies. J. W. Mancillas
Section A
Unknown Site
8:30 Introductory Remarks.
8:40 204. Semiempirical
Calculation of Crystal Structures. J. J. P. Stewart
9:20 205. Semiempirical quantum chemistry: Where we are and where we are going.
K. M. Merz Jr.
10:00 206. Semi-empirical parameters for
transition metals. W. J. Hehre, J. Yu
10:40 Intermission.
10:55 207. Semi-empirical modeling of transition metal
complexes. C. Buda, T. Cundari
11:35 208. Progress
towards a "next generation" NDDO-based semiempirical technique. T. Clark,
P. Winget, C. Selcuki, A. Horn, B. Martin
Section B
Unknown Site
8:55 Introductory Remarks.
9:00 209. Insight into
the docking of metalloproteinases. X. Hu, W. H. Shelver
9:30 210. Protonation-induced stereoisomerism in tertiary amines: Application of
QM-based molecular dynamics methods. P. S. Hammond, R. Car, R. Harris, W.
S. Caldwell, J. D. Schmitt
10:00 Intermission.
10:15 211. Tautomerism of nucleobase derivatives and their score in virtual
screening to thymidine kinase. P. Pospisil, P. Ballmer, G. Folkers, L.
Scapozza
10:45 212. Generating pharmacophore queries and small
molecule representations for Virtual Screening. E. K. Davies, C. J.
Davies
Section C
Unknown Site
8:00 213. Electronic structure and chemical potentials of molecules
in spc/e water. R. M. Lynden-Bell, S. Murdock
8:40 214.
Predicting Absolute Free Energies of Solvation for the Proton and the Hydroxide
Ion. D. A. Dixon, D. F. Feller, C. Zhan, J. S. Francisco
9:20 215. Generalized Born continuum solvation models for protein structure
prediction. R. A. Friesner
10:00 Intermission.
10:15 216. Towards ab Initio cavities for dielectric continuum
solvation models. M. Dupuis, D. M. Camaioni, D. M. Chipman, J.
Bentley
10:55 217. Charge flow and solvent dynamics in the
photodissociation of molecular anions. R. Parson, N. Delaney, J. Faeder,
M. Thompson
11:35 218. Continum and hybrid solvent models based
on the finite-difference Poisson-Boltzmann method. R. Luo
Section D
Unknown Site
8:30 219. Evaluating protein-ligand interactions through flexible
docking. T. Hurst
8:55 220. Affinity based high
throughput screening of orphan targets: Practical solutions for removing
promiscuous binders. K. M. Comess, M. J. Voorbach, M. L. Coen, H. Tang,
L. Gao, X. Cheng, M. E. Schurdak, B. A. Beutel, D. J. Burns
9:20 221. Computational solvent mapping for the analysis of enzyme active sites.
S. Vajda, S. Dennis, T. Kortvelyesi, M. Silberstein, K.
Clodfelter
9:45 222. THEMATICS: Identification and
characterization of active sites from structure alone. M. J. Ondrechen,
J. G. Clifton, D. Ringe
10:10 Intermission.
10:25 223. Identification of a second binding site in the Estrogen Receptor. W.
P. van Hoorn
10:50 224. Supramolecular transport of retinol
and fenretinide: implications in breast cancer. A. M. Waligorski, J. D.
Evanseck
11:15 225. QM and mixed QM/MM simulations of model
nerve agents with acetylcholinesterase. J. B. Wright, M. M. Hurley, G.
Lushington, W. E. White, J. A. Morrill
Section A
Unknown Site
1:30 Introductory Remarks.
1:35 226. Volume change
studies using quantum mechanically derived QSPR. A. J. Holder, D. A.
White, R. Smith, C. C. Chappelow, C. Pinzino, J. D. Eick, J. A.
Morrill
2:00 227. Topologically interesting molecules with only
one side. M. M. Francl, D. Kalyani
2:25 228. Model for
solubility parameter predictions derived by QSPR. A. J. Holder, J. D. Eick,
J. E. Code, C. C. Chappelow
2:50 229. Semi-Empirical
Calculations of Rod-Like Dinuclear Ruthenium Complexes for Dye Sensitized
Photovoltaic Applications. J. Walker, L. Samuelson, R. Mosurkal, J.
Kumar
3:15 Intermission.
3:30 230.
Semiempirical study of the mechanism of cationic homopolymerization and
copolymerization of monomer systems. A. J. Holder, M. D. Miller, J. D.
Eick, C. C. Chappelow
3:55 231. Semiempirical calculations of
reactive surfaces for twisted intramolecular charge transfer (TICT). M.
Maroncelli, W. Song
Section B
Unknown Site
1:25 Introductory Remarks.
1:30 232. ProtoPlex:
User-control over tautomeric and protonation state. R. S. Pearlman, R.
Khashan, D. Wong, R. Balducci
2:00 233. A Tautomer and
Protonation Pre-Processor for Virtual Screening. J.
Sadowski
2:30 234. To clean or not to clean? The question of
appropriate structural representation in corporate databases M. J.
Polley, J. T. Swanson, W. Homer, R. D. Clark
3:00
Intermission.
3:15 235. Automated database ionization.
J. Klicic, M. Reboul
3:45 236. Hooked on protonics. R.
Sayle, G. Skillman
4:15 Panel Discussion.
Section C
Unknown Site
1:30 237. Ab-initio simulations of simple aqueous solutions. G.
Galli, E. R. Schwegler, J. C. Grossman
2:10 238. Ab Initio
Molecular Dynamics Studies of Ion-water Interactions. D. J. Tobias, I. W.
Kuo, C. J. Mundy
2:50 239. Treating manybody dispersion and
polarization within a unified formalism. G. Martyna, T.
Whitfield
3:30 Intermission.
3:45 240. First
principles study of aqueous hydroxide solutions. B. Chen, I. Ivanov, M.
L. Klein
4:25 241. Rapid calculation of free energy and solution
structure with high level ab initio models of solute-water interactions. W.
Liu, R. H. Wood, D. J. Doren
4:45 242. Ab initio molecular
dynamics via a novel combination of discrete variable representations and plane
wave basis sets. Y. Liu, M. E. Tuckerman
Section D
Unknown Site
1:30 243. Chemometrics: Past, Present, and Future B. K.
Lavine, J. Workman Jr.
2:10 244. Transferring and Improving
the Robustness of Multivariate Calibrations. S. D. Brown, H. Tan, R.
Feudale, T. Myles
2:50 245. Application of Modified Alternating
Least-Squares (MALS) Regression to Spectroscopic Image Analysis. T. M.
Hancewicz, S. L. Zhang, P. Hopke, J. -. Wang
3:30 246.
Chemometric tools in bioinformatics. A. Berglund, F.
Pettersson
4:10 247. Mapping protein energy landscapes by
chemometric methods. J. D. Evanseck, B. G. Schulze
Section A
Unknown Site
8:30 Introductory Remarks.
8:35 248. Natural bond orbital evaluation of AM1-predicted C-H O hydrogen bonds in dimers of 1,5,7,11-tetraoxaspiro[5.5]undecane A. J. Holder, C. D.
Harris
9:00 249. The use of semiempirical methods for
conformational studies of novel angiogensis inhibitors. J. P. Bowen, S.
Furness, T. P. Robinson, T. Ehlers, R. Hubbard IV, C. Fowler, J. L. Arbiser, D.
Goldsmith
9:25 250. QSAR model from semiempirical methods to
predict induction of the CYP1A1 gene. A. J. Holder, K. M. Andreasen, D.
M. Yourtee, J. D. Eick, C. C. Chappelow
9:50 Intermission.
10:05 251. New semiempirical quantum methods for biological
reactivity. D. M. York
10:30 252. New Semiempirical
Method for fast and accurate protein modeling. N. Anikine, V. Bugaenko, V.
Bobrikov, A. Andreyev, V. M. Anisimov
10:55 253. Quantum
mechanically derived QSARs for reversible inhibitors of acetylcholinesterase.
J. A. Morrill, J. B. Wright, M. M. Hurley, W. E. White
Section B
Unknown Site
8:30 254. Prediction of protein retention times in anion exchange
chromatography systems using support vector machine regression. M. Song,
J. Bi, C. M. Breneman, N. Tugcu, N. Sukumar, K. P. Bennett, S. M.
Cramer
9:10 255. On the effectiveness of bootstrap aggregation
for constructing neural network ensembles for QSAR and QSPR. D. K.
Agrafiotis, W. Cedeno, V. S. Lobanov
9:50 256. Optimization
of MDL substructure search keys for the prediction of activity and toxicity.
D. R. Henry, J. L. Durant Jr.
10:30 257. Asymmetric
Clustering of Chemical Datasets: An Investigation. J. D. MacCuish, N. E.
MacCuish
11:10 258. Genetic algorithms for developing
structure-activity correlations in large pharmaceutical and olfactory databases.
B. K. Lavine, C. E. Davidson, C. Breneman, W. Kaat
Section C
Unknown Site
8:00 259. Solvation in microheterogeneous fluids. J. I.
Siepmann, B. Chen, C. D. Wick, J. M. Stubbs, L. Sun
8:40 260. Good + bad = bad: Forward and reverse FEP calculations should not be
averaged. D. A. Kofke, N. Lu
9:20 261. Parallel tempering
Monte Carlo simulations of (H2O)n,
(H2O)n+, and (CO2)n
clusters K. D. Jordan
10:00 Intermission.
10:15 262. Solvation thermodynamics of small ionic water
clusters relevant to nucleation. S. M. Kathmann, G. K. Schenter, B. C.
Garrett
10:55 263. Novel phase behavior of water inside nanotube
and slit nanopore. X. C. Zeng, K. Koga, G. T. Gao, H.
Tanaka
11:35 264. Hydration free energies and entropies of water
in protein interiors. S. Rick, L. R. Olano
Section D
Unknown Site
8:30 265. Effect of ion binding on the conformational dynamics of
calmodulin. Y. Y. Sham, R. Zhou, F. Suits, R. Germain
8:55 266. Direct observation of the folding and unfolding of a b-hairpin in
explicit water through computer simulation. X. Wu, S. Wang, B. R.
Brooks
9:20 267. Computational structural proteomics: Guiding
mutagenesis experiments with rigid body dynamics and B-splines. R. E.
Gillilan, L. You, T. Huffaker
9:45 Intermission.
10:00 268. High-Throughput Data Analysis. D.
Rogers
10:25 269. Computational design of biomimetic
materials. B. Chen, R. J. Doerksen, M. L. Klein
10:50 270. Structural basis for the resistance of oligonucleotides containing
NNK-induced O6-[4-oxo-4-(3pyridyl)butyl]guanine adducts to 3â¨5â exonucleases. M. Seetharaman, A. Ogdie, S. Park,
D. M. Ferguson, N. Tretyakova
11:15 271. Adaptive wavelet
thresholding for denoising DNA microarrays. C. S. Uehara, A. H. Spexet,
I. A. Kakadiaris
Section A
Unknown Site
1:30 272. Summation approximants: An easy way to improve the
accuracy of ab initio quantum chemistry. D. Z. Goodson
1:50 273. Efficient parallelization of SCF and DFT analytic second derivatives.
T. L. Windus, E. Apra, R. J. Harrison, B. G. Johnson
2:10 274. Intermolecular and Intramolecular Energy Transfer in Ne-atom Collisions
with a n-Hexylthiolate Self-Assembled Monolayer (SAM). T. Yan, W. L.
Hase
2:30 275. Computer-aided construction of
pressure-dependent reaction networks for large, gas-phase chemical
mechanisms D. M. Matheu, W. H. Green Jr., J. M. Grenda
2:50 276. Functionality Mapping as a Method to Identify Stereocontrol Elements
for Asymmetric Reactions. M. Panda, M. C. Kozlowski
3:10 277. An algorithm for conformational sampling using distance constraints.
H. Xu, D. Agrafiotis
Section B
Unknown Site
1:30 278. Machine learning models for highly-multidimensional
molecular descriptors. J. Yu, W. Mydlowec
2:10 279.
SARstep: A novel conceptual framework for QSAR. L. W. Herman, D. Clemens,
A. Caracoti
2:50 280. From decision tree to decision forest ö a
novel chemometrics approach for QSAR study. W. Tong, H. Hong, H. Fang, Q.
Xie, R. Perkins
3:30 281. Early prediction of bioavailability by
Adaptive Fuzzy Partitioning (AFP). M. Pintore, N. Piclin, H. van de Waterbeemd,
J. R. Chretien
4:10 282. On the effectiveness of
bootstrap aggregation for constructing neural network ensembles for QSAR and
QSPR. D. K. Agrafiotis, S. Izrailev, W. Cedeno
Section C
Unknown Site
1:00 283. Novel method of Ab Initio evaluation of the pseudo
Jahn-Teller effect. I. B. Bersuker, N. Balabanov, D. Pekker, J. E.
Boggs
1:25 284. b-X elimination in
Ta(H)2(OH)3: A density functional theory study. C. D.
Taylor, T. R. Cundari
1:50 285. DFT and ONIOM modeling of
the Suzuki cross-coupling reaction, Pd vs. Ni Y. Zhao, T.
Cundari
2:15 286. Computational study of solvolysis reactions
using the explicit solvent model. J. Mareda, J. Fuchs, M.
Rizzello
2:40 287. Interaction model for functional groups using
properties found in quantum calculations. S. G. Arturo, D. E.
Knox
3:05 Intermission.
3:15 288. Predictive
modeling of chemical reactions. L. J. Soltzberg, N. E. Lee, A. Honda, M.
Sanford, M. Sekoni
3:40 289. Polarization and dynamics of water
and Schiff Base within bacteriorhodopsin. I. W. Kuo, C. J. Mundy, D. J.
Tobias
4:05 290. Theoretical investigation of the structure and
vibrational frequencies of homogeneous and heterogeneous clusters of HPLC
solvents: Water, methanol, and acetonitrile J. M. Craig, D. D. Shillady,
S. C. Rutan, S. S. Hunnicutt, E. Bezemer
4:30 291.
Intermolecular potentials for gas hydrates obtained from ab initio
quantum mechanics. J. B. Klauda, S. I. Sandler