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COMP Programming

Fall 2003 National Meeting
Final Program
226th ACS National Meeting
New York, NY
September 7-11, 2003

R. A. Wheeler and W. D. Cornell, Program Chair
SOCIAL EVENT:
Poster Session/Social Hour, Tue
Presentation of CCG Excellence Awards: Tue
BUSINESS MEETING: Sat

SUNDAY MORNING
Section A
Javits Convention Center -- 1E11

Frontiers in DNA Research: An Interdisciplinary Symposium

Drug-DNA Interactions: Part I

J. D. Evanseck and S. M. Firestine, Organizers

8:00 — Introductory Remarks.

8:45 —1. G-Quadruplexes: their importance in gene silencing, as targets for drug design, and in the etiology of colorectal cancer. L. H. Hurley

9:30 —2. Programmed read-out of the DNA minor groove by synthetic ligands. P. B. Dervan

10:15 — Intermission.

10:30 —3. Threading polyintercalation. B. L. Iverson, J. Lee, V. Guelev

11:15 —4. Controlling nucleic acid structural transitions by intercalation. N. V. Hud, S. Jain

SUNDAY MORNING
Section B
Javits Convention Center -- 1E13

Parallel and High-Performance Computing in Chemistry

Methods and Algorithms

D. E. Bernholdt, Organizer, Presiding

8:30 — Introductory Remarks.

8:35 —5. Parallelization of the effective fragment method for solvation and extensions to model bulk behavior. H. Netzloff, M. S. Gordon

9:20 —6. Large scale parallelization of the plane wave based ab initio MD method. G. Martyna, M. Tuckerman, L. Kale, R. Vadali

10:05 — Intermission.

10:20 —7. High performance computing with NWChem. T. L. Windus, E. Apra, S. Hirata, E. J. Bylaska, T. P. Straatsma

11:05 —8. Parallelization of linear-scaling Fock matrix builds. C. K. Gan, V. Weber, M. Challacombe

SUNDAY MORNING
Section C
Javits Convention Center -- 1E12

Theory and Simulation of Protein Folding Kinetics

J. Pitera, Organizer

8:30 — Introductory Remarks.

8:40 —9. Folding@Home: Can non-equilibrium statistical mechanics and 100,000 CPUs simulate protein folding in atomic detail on the millisecond timescale? V. S. Pande

9:10 —10. Effects of confinement in chaperonin-assisted protein folding: rate enhancement through smoothing of the folding energy landscape. A. Baumketner, A. Jewett, J. Shea

9:40 —11. Comparing simulations of the kinetics and thermodynamics of peptide folding. C. Simmerling, A. E. Roitberg, G. Cui

10:10 — Intermission.

10:25 —12. Peptide dynamics from microsecond molecular dynamics simulations in explicit solvent. I. Yeh, G. Hummer

10:55 —13. TBA. C. Clementi

11:25 —14. Probing the principles of amyloid peptide aggregation. J. E. Straub

SUNDAY AFTERNOON
Section A
Javits Convention Center -- 1E11

Frontiers in DNA Research: An Interdisciplinary Symposium

DNA Structure and Function: Part I

J. D. Evanseck and S. M. Firestine, Organizers

1:00 — Introductory Remarks.

1:45 —15. DNA bulges: Coordinates and free energies. B. M. Pettitt, M. Feig

2:30 —16. Measuring the global structure and mechanical properties of DNA and the relation to protein-DNA complexes. D. M. Crothers, Y. Zhang

3:15 — Intermission.

3:30 —17. DNA bending and flexibility in simple and not-so-simple systems. L. J. Maher III

4:15 —18. Deterministic path sampling of the closing conformational transition of DNA polymerase beta. T. Schlick, R. Radhakrishnan

5:00 —19. Fuzzy bar code representations of DNA-protein interactions. N. Sukumar, C. M. Breneman, C. Lawrence, K. P. Bennett, I. Vitol

SUNDAY AFTERNOON
Section B
Javits Convention Center -- 1E13

Parallel and High-Performance Computing in Chemistry

Emerging Hardware and Software Technologies

T. L. Windus, Presiding
D. E. Bernholdt, Organizer

1:30 — Introductory Remarks.

1:35 —20. Report on an efficient conformational space search method using parallel computing and grid technology. H. Goto, K. Ohta, M. Sato, T. Boku, U. Nagashima, H. Chuman

2:20 —21. Effective VHTS using compute grids. C. Crafford

3:05 — Intermission.

3:20 —22. Synthesizing highly optimized code for correlated electronic structure calculations. D. E. Bernholdt, A. Auer, G. Baumgartner, A. Bibireata, V. Choppella, D. Cociorva, X. Gao, R. J. Harrison, S. Hirata, S. Krishnamoorthy, S. Krishnan, C. Lam, Q. Lu, M. Nooijen, R. M. Pitzer, J. Ramanujam, P. Sadayappan, A. Sibiryakov

4:05 —23. Hijacking the PlayStation2 for computational chemistry. B. Levine, T. J. Martinez

SUNDAY AFTERNOON
Section C
Javits Convention Center -- 1E12

Theory and Simulation of Protein Folding Kinetics

J. Pitera, Organizer

1:30 — Introductory Remarks.

1:40 —24. Folding dynamics, statistics and paths. J. Wang

2:10 —25. Learning folding & domain swapping from all-atom structures and simple parametes. A. Linhananta, H. Zhou, C. Zhang, Y. Zhou

2:40 —26. Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide. S. Chowdhury, W. Zhang, C. Wu, G. Xiong, Y. Duan

3:10 — Intermission.

3:20 —27. Conformational changes and folding pathways of proteins computed using the stochastic difference equation. A. E. Cardenas, R. Elber

3:50 —28. Extracting dynamical information about protein folding from time series analysis. K. Kostov, M. Toda, Y. Matsunaga, T. Komatsuzaki

4:20 —29. Constructing master equation models of protein dynamics from parallel tempering simulations. J. D. Chodera, K. A. Dill

4:50 — Concluding Remarks.

SUNDAY AFTERNOON
Section D
Javits Convention Center -- 1E04

Challenges for the Chemical Sciences in the 21st Century: Information and Communication

P. Gund, Organizer, Presiding

1:30 — Introductory Remarks.

1:35 —30. Purposes of the NRC report, "Challenges for the chemical sciences in the 21st century". D. J. Raber

1:40 —31. Challenges for the chemical sciences in the 21st century: a workshop report. M. Ratner, R. C. Alkire

2:10 —32. Advancing chemical science and technology through information technologies. T. H. Dunning Jr.

2:40 — Intermission.

2:50 —33. How scientific computing, knowledge management, and databases can enable advances and new insights in chemical technology. A. M. Chaka

3:20 —34. Drug Discovery, a game of 20 Questions. D. J. Underwood

3:50 —35. Modeling of complex chemical systems relevant to biology and pharmaceutical research: problems and prospects. R. A. Friesner

4:20 — Discussion.

MONDAY MORNING
Section A
Javits Convention Center -- 1E11

Frontiers in DNA Research: An Interdisciplinary Symposium

Artifical Control of Gene Expression

J. D. Evanseck and S. M. Firestine, Organizers

8:00 — Introductory Remarks.

8:45 —36. Studies toward the artifical control of gene expression. S. M. Firestine, N. Lin, D. Bednarski, J. Hooda, S. Mueller, J. D. Evanseck, A. Loccisano

9:30 —37. Towards a molecular picture of gene expression: mapping the regulatory surfaces of the transcriptional machinery. A. K. Mapp, A. R. Minter, J. K. Lum, G. belanger, B. B. Brennan, Z. Wu, A. Plachetka, S. P. Rowe

10:15 — Intermission.

10:30 —38. Designer polydactyl zinc finger proteins: Development of a universal system for gene addressing and regulation. C. F. Barbas III

11:15 —39. Ternary complex of DNA, CAP, and lac repressor: Multi-scale structural model and simulation perspectives. A. Balaeff, L. Mahadevan, K. Schulten

MONDAY MORNING
Section B
Javits Convention Center -- 1E13

Parallel and High-Performance Computing in Chemistry

Applications

R. J. H. Harrison, Presiding
D. E. Bernholdt, Organizer

9:00 — Introductory Remarks.

9:05 —40. Application of parallel processing methods in Monte Carlo simulations of molecular clusters. K. D. Jordan

9:50 —41. Parallel computational chemical calculations for Air Force material projects. J. Blaudeau, D. S. Dudis, A. T. Yeates, T. M. Cooper

10:35 —42. Numerical methods for time-dependent Schroedinger equations in the nonlinear-nonperturbative regime of laser-molecule interactions. A. D. Bandrauk, H. Lu

MONDAY MORNING
Section C
Javits Convention Center -- 1E12

Modeling Spin Forbidden and Open-Shell Processes

T. Cundari and N. Matsunaga, Organizers

8:30 — Introductory Remarks.

8:40 —43. The spin-orbit interaction and conical intersections. A new look at an old problem. D. R. Yarkony

9:20 —44. Very-large-core relativistic effective potentials for calculations of electronic spectra. W. C. Ermler, M. M. Marino

10:00 — Intermission .

10:15 —45. Ultrafast cage-induced spin flip processes in molecular photodissociation in matrices and clusters. R. B. Gerber, M. Y. Niv, A. Cohen

10:55 —46. Relativistic potential energy surfaces and laser control of chemical reactions. S. Koseki

MONDAY MORNING
Section D
Javits Convention Center -- 1E04

Computational Chemistry in Drug Discovery: Are High Information Content Calculations Better than Low Information Content Calculations?

Cosponsored with CINF
J. L. Miller, Organizer

8:00 — Introductory Remarks.

8:10 —47. Are high information content calculations better than low information content calculations? From 2D/3D descriptors to scoring functions, pharmacophores and molecular orbitals. A. A. Alex, J. E. J. Mills, M. J. de Groot

8:35 —48. Integrating vHTS into combinatorial library design. R. D. Clark, D. S. Baker, L. Akella, F. Soltanshahi

9:00 —49. Comparing computational approaches to screening library selection. E. Evensen, H. Purkey, K. Lind, E. K. Bradley

9:25 —50. Assessing the effect of library design choices on model performance. K. Aumond, H. Wolters, J. L. Miller

9:50 — Intermission.

10:00 —51. HTSview: Software which leads to lead ideas. M. Zimmermann, S. A. Hindle, T. Naumann, H. Matter, G. Hessler, K. Baringhaus, C. Lemmen, M. Gastreich, M. Rarey

10:25 —52. Probing information content in QSAR analyses using the signature molecular descriptor. J. Faulon, S. Martin, D. P. Visco, A. Kotu

10:50 —53. Modeling the mu-opiod receptor affinity of synthetic 8-aminocyclazocine analogues using TAE, PEST and PAD descriptors and machine-learning methods. L. Shen, C. M. Breneman, N. Sukumar, M. P. Wentland, M. J. Embrechts

11:15 —54. Fleshing-out pharmacophores with volume rendering of molecular charge densities and hyperwall visualization technology. P. J. MacDougall, C. E. Henze

MONDAY AFTERNOON
Section A
Javits Convention Center -- 1E11

Frontiers in Biophysical Methods

Novel Spectroscopies and Microscopies

Cosponsored with PHYS

Frontiers in DNA Research: An Interdisciplinary Symposium

DNA-Protein Interactions

J. D. Evanseck and S. M. Firestine, Organizers

1:00 — Introductory Remarks.

1:45 —55. Internal coordinate molecular dynamics (ICMD) modeling of DNA under limited hydration. A. K. Mazur

2:30 —56. Azole carboxamide nucleobases as probes or nucleic acid polymerases. V. J. Davisson, D. E. Bergstrom

3:15 — Intermission.

3:30 —57. Computational studies of base flipping in DNA alone and bound to the cytosine-5-methyltransferase from HhaI. A. D. MacKerell Jr.

4:15 —58. Analysis and control of protein-DNA loops. J. D. Kahn, L. M. Edelman, R. Cheong, R. A. Mehta

5:00 —59. Anomalous migration of intrinsically curved DNA. U. Mohanty, A. Spasic

MONDAY AFTERNOON
Section B
Javits Convention Center -- 1E13

Computational Chemistry in Drug Discovery: Are High Information Content Calculations Better than Low Information Content Calculations?

Cosponsored with CINF
J. L. Miller, Organizer

1:30 —60. Merging tethered binding data and informative descriptor analysis to identify potential sites of small molecule binding. E. K. Bradley, E. Evensen, H. Purkey, K. Lind, A. C. Braisted, M. R. Arkin

1:55 —61. Enrichment factors in molecular docking: Common misconceptions. A. Filikov

2:20 —62. Incorporating explicit hydration into computational drug design. R. L. Mancera

2:45 — Intermission.

2:55 —63. Molecular dynamics simulations studies on human coagulation factor Va. T. Orban, V. Gogonea, M. Kalafatis

3:20 —64. Lead optimization: using MD to improve potency and selectivity in PTP-1B inhibitors. C. I. Bayly, C. K. Lau, J. Y. Gauthier, C. Li, M. ThŽrien, E. Asante-Appiah, W. Cromlish, Y. Boie, F. Forghani, S. Desmarais, Q. Wang, K. Skorey, D. Waddleton, P. Payette, C. Ramachandran, B. Kennedy, G. Scapin

3:45 —65. COSMO-RS: A novel bridge from quantum chemistry to fluid phase thermodynamics. A. Klamt

4:10 —66. First Principles calculation of drug solubility, partitioning, and pKa with DFT/COSMOtherm: Getting insight, not just numbers. A. Klamt

4:35 —67. Accurate prediction of protein – ligand binding energy in the QCPFF approach. N. A. Anikin, V. V. Bobrikov, V. L. Bugaenko, A. M. Andreyev, V. M. Anisimov

MONDAY AFTERNOON
Section C
Javits Convention Center -- 1E12

Modeling Spin Forbidden and Open-Shell Processes

T. Cundari and N. Matsunaga, Organizers

1:30 —68. Role of the minimum on the seam of crossing (MSX) between different spin states in spin-forbidden reactions. K. Morokuma

2:10 — Intermission .

2:20 —69. Spin-forbidden reactions in organometallic chemistry: How fast do they really go? J. N. Harvey, R. Poli

3:00 —70. Catalysis by paramagnetic chromium complexes: Rational design of catalysts in spin-forbidden reactions. D. J. Doren, D. R. Fitzgerald, J. S. Hess

3:40 —71. Modeling of open-shell species. T. R. Cundari

Frontiers in Biophysical Methods

Manipulation and Fluorescence of Single Biomolecules

Cosponsored with PHYS

MONDAY EVENING
Section A
Javits Convention Center -- North Pavillion

Sci-Mix

R. A. Wheeler, Organizer

8:00 - 10:00

106, 111, 114, 120-121, 126, 132-134, 137-138, 142-144, 146-148, 153, 155, 159, 162-163, 170, 172, 175-176. See subsequent listings.

TUESDAY MORNING
Section A
Javits Convention Center -- 1E11

Frontiers in DNA Research: An Interdisciplinary Symposium

Drug-DNA Interactions: Part II-Sequence Recognition

J. D. Evanseck and S. M. Firestine, Organizers

8:00 — Introductory Remarks.

8:45 —72. Natural products and nature's lessons: five solutions to the sequence selective recognition of duplex DNA. D. Boger

9:30 —73. Characterizing the molecular recognition of Watson-Crick and T/G mismatched base pairs by stacked polyamides. M. Lee, M. Le, J. Grandillo, K. Buchmueller, S. Horick, W. D. Wilson, A. Staples, E. Lacy, B. Nguyen, C. O'Hare, J. A. Hartley

10:15 — Intermission.

10:30 —74. Hybridization of complementary and homologous peptide nucleic acid probes to folded DNA targets. B. A. Armitage, S. A. Kushon, B. Datta, C. Schmitt, J. P. Jordan

11:15 —75. Quantitative representation of DNA-ligand interactions. W. K. Olson

TUESDAY MORNING
Section B
Javits Convention Center -- 1E13

Structure Based Drug Design in Signal Transduction and Cell Cycle

Structural Studies of Tyrosine Kinases

E. Lunney and G. M. Verkhivker, Organizers

8:00 —76. Conformational targeting of Abl kinase using small molecule inhibitors. W. G. Bornmann, D. Veach

8:35 —77. Development of a curative treatment program for chronic myelogenous leukemia (CML). B. Clarkson, D. Veach, W. G. Bornmann

9:10 —78. Crystal structure of unphosphorylated c-Src in complex with an analogue of GleevecTM reveals relative orientations of the SH3, SH2 and kinase domains in the active conformation. S. W. Cowan-Jacob, G. Fendrich, J. Liebetanz, D. Fabbro, P. W. Manley

9:45 — Intermission.

10:00 —79. Structure-based methods to design potent and selective Src/Abl dual inhibitors and their development as antileukemic and antimetastatic agents. C. Metcalf III, Y. Wang, W. Shakespeare, R. Sundaramoorthi, T. Keenan, D. Dalgarno, R. Bohacek, K. Burns, J. Roses, M. R. van Schravendijk, M. Ram, J. Keats, S. Liou, S. Adams, J. Snodgrass, V. Rivera, M. Weigele, J. Iuliucci, T. Clackson, M. Frame, V. Brunton, T. Sawyer

10:35 —80. Structure of apo, unactivated insulin-like growth factor 1 receptor kinase at 1.5 resolution. S. Munshi

11:10 —81. EGF receptor kinase domain A-loop is poised for catalysis without tyrosine phosphorylation. C. Eigenbrot, J. Stamos, M. X. Sliwkowski

TUESDAY MORNING
Section C
Javits Convention Center -- 1E12

Modeling Spin Forbidden and Open-Shell Processes

T. Cundari and N. Matsunaga, Organizers

8:30 —82. Energy splittings of different spin states: A challenge for modern quantum chemical methods in transition metal chemistry. M. Reiher

9:10 —83. Reduction of oxomanganese (V) porphyrins by bromide ions: a DFT study. F. De Angelis, R. Car, N. Jin, J. T. Groves

9:50 — Intermission .

10:00 —84. Structural prediction of transition metal tetrachlorides by semiempirical and DFT methods. C. Buda, T. Cundari

10:40 —85. Beyond the two-state conical intersections: Three-state conical intersections in the allyl radical. S. Matsika, D. R. Yarkony

11:20 —86. Stability of pyrimidine nucleic acid bases with respect to intra- and intermolecular proton transfer reactions induced by excess electrons. M. Gutowski, I. Dabkowska, M. Haranczyk, J. Rak, K. H. Bowen Jr., S. Xu, J. M. Nilles, D. Radisic, S. Stokes

Frontiers in Biophysical Methods

Manipulation and Fluorescence of Single Biomolecules

Cosponsored with PHYS

Computational Toxicology

Cosponsored with TOXI

TUESDAY AFTERNOON
Section A
Javits Convention Center -- 1E11

Frontiers in DNA Research: An Interdisciplinary Symposium

DNA Structure and Function: Part II

J. D. Evanseck and S. M. Firestine, Organizers

1:00 — Introductory Remarks.

1:45 —87. Impact of minor groove functional groups on DNA structure. L. W. McLaughlin, T. Lan, D. Chen, A. Fraley

2:30 —88. Molecular dynamics simulations of Papilloma Virus E2 DNA sequences: Dynamical models for oligonucleotide structures in solution. K. S. Byun, D. L. Beveridge

3:15 — Intermission.

3:30 —89. DNA quadruplexes: structures and their recognition. S. Neidle, G. N. Parkinson, M. Lee, G. Chessari, S. Haider

4:15 —90. Structural characterization of N-acetyl-2-aminofluorene (AAF) guanine and deoxyguanosine adducts via a molecular mechanics, semi-empirical, and density functional theory cascade method. T. A. Isgro, N. Mathew, R. Q. Topper

5:00 —91. Step-wise assembly of DNA tilings and their applications. S. J. Ahn, S. H. Park, H. Yan, J. H. Reif, T. H. LaBean

TUESDAY AFTERNOON
Section B
Javits Convention Center -- 1E13

Structure Based Drug Design in Signal Transduction and Cell Cycle

Structural Studies of Kinases

E. Lunney and G. M. Verkhivker, Organizers

1:00 —92. Design of MAP kinases inhibitors for the treatment of inflammatory diseases. F. G. Salituro

1:35 —93. Binding modes of known classes of p38 MAP kinase inhibitors. N. Moss

2:10 —94. Human map kinase kinase 1 (MEK1): De novo crystal structure determination and structure-based drug design. J. F. Ohren, C. E. Whitehead, E. Zhang, A. Pavlovsky, H. Chen, P. Kuffa, C. Yan, P. McConnell, A. Delaney, N. Y. Chirgadze, C. Hasemann

2:45 — Intermission.

3:00 —95. Structure-based design of highly potent and selective cdk4 inhibitors. T. Honma, K. Hayashi, T. Yoshizumi, C. Ikeura, M. Ikuta, I. Suzuki-Takahashi

3:35 —96. Importance of Cation-p interactions for molecular recognition of ATP in ATP-binding proteins. L. Mao, Y. Wang, Y. Liu, X. Hu

4:10 —97. Structure-based drug design with PDK1. D. M. F. van Aalten

TUESDAY AFTERNOON
Section C
Javits Convention Center -- 1E12

Emerging Technologies in Computational Chemistry

Cosponsored with Schrodinger Inc
C. M. Breneman, Organizer

1:00 — Introductory Remarks.

1:10 —98. Mining molecular dynamics data for molecular properties. R. A. Wheeler

1:40 —99. Super-linear minimization scheme for the nudged elastic band method. J. Chu, B. Trout, B. R. Brooks

2:10 —100. Peptide to non-peptide: A real breakthrough in virtual screening. J. G. Vinter, T. J. Cheeseright, M. D. Mackey

2:40 —101. Implementation and development of the self-consistent charge density functional tight-binding method. M. Gutowski

3:10 — Intermission.

3:25 —102. Prediction and classification of protein binding sites. M. Keil, T. Exner, J. Brickman

3:55 —103. QSAR-based database mining: A success story of the discovery and experimental validation of novel anticonvulsant compounds. M. Shen, C. Beguin, A. Golbraikh, H. Kohn, A. Tropsha

4:25 —104. Stochastic proximity embedding – methods and applications. H. Xu, D. K. Agrafiotis

4:55 — Presentation of Best Paper Award.

TUESDAY EVENING
Section A
Javits Convention Center -- North Pavillion

Computers in Chemistry Posters

R. A. Wheeler and W. D. Cornell, Organizers

6:00 - 8:00

105. Automatic synthesis of high-performance parallel programs for electronic structure methods. P. Sadayappan, A. Auer, G. Baumgartner, D. E. Bernholdt, A. Bibireata, D. Cociorva, V. Choppella, X. Gao, R. J. Harrison, S. Hirata, S. Krishanmoorthy, S. Krishnan, C. Lam, Q. Lu, M. Nooijen, R. M. Pitzer, J. Ramanujam, A. Sibiryakov

106. Theoretical investigations of systems relevant in the chemistry of the atmosphere. M. Rosi, M. Di Stefano, A. Sgamellotti

107. Low lying electronic states of HOCl cation: Ab initio calculations and simulations of the He I photoelectron spectrum. D. K. W. Mok, A. K. T. Yeung, D. Wang, F. Chau

108. Dynamics of methylene nitramine decomposition from reaction path calculations. C. Stopera, D. Thweatt, M. Page

109. A new mechanism for photodesorption: Self-trapping of surface excitons. M. A. Gabriel, W. Stier, F. D. Vila, G. Henkelman, H. Jonsson

110. Screening tools for the design of molecular diodes. S. K. Pollack

111. Electronic structure of 1 to 2 nm diameter silicon core/shell nanocrystals: Surface chemistry, optical spectra, and doping. Z. Zhou, L. Brus, R. A. Friesner

112. Semi-DFT approach to calculation of protein systems. N. A. Anikin, V. L. Bugaenko, V. M. Anisimov

113. A study of chemical stability of novel, potent inhibitors of DPP-IV. D. Sitkoff, D. Magnin, J. Robl, R. B. Sulsky, D. J. Augeri, Y. Huang, P. Taunk, D. A. Betebenner, L. M. Simpkins, J. G. Robertson, A. Khanna, B. Abboa-Offei, A. Wang, M. Cap, L. Xing, L. Tao, M. Malley, J. Z. Gougoutas, Q. Huang, S. Han, R. A. Parker, L. G. Hamann

114. In silico structural models for the end states of ATP hydrolysis in the motor protein myosin. S. M. Schwarzl, J. C. Smith, S. Fischer

115. Functions of the copper(I)-thiolate cluster in CopY. M. A. Harrison, J. D. Evanseck, C. T. Dameron

116. A DFT Investigation of the remarkable reactivity of the gem-dizinc (IZn)2(CHI carbenoid as a cyclopropanation reagent compared to the mono zinc IZnCHI2 carbenoid. D. Wang, C. Zhao, D. L. Phillips

117. Reactivity and spectra of model cytochrome P450 intermediates. J. C. Hackett, R. W. Brueggemeier, C. M. Hadad

118. Ab initio studies of the energies, structures and electronic properties of myo-inositol mono-phosphate in-vacuo and water. P. Yang, X. Bai, P. P. N. Murthy, R. E. Brown

119. Predicting aqueous solubility: A fundamental approach. J. D. Thompson, C. J. Cramer, D. G. Truhlar

120. Contribution of ordered water molecules to binding thermodynamics. Z. Li, T. Lazaridis

121. Solubility of CO2 in brines through FEP/MC simulations. T. J. Dick, J. D. Madura

122. A Priori pKa predictions: Investigation of steric effects on the basicity of substituted pyridines via MC/FEP calculations. T. M. Lyons, I. Tubert-Brohman, W. L. Jorgensen

123. Solvated vs. dipole-bound electron from the point of view of Atoms-In-Molecule theory. Q. K. Timerghazin, G. H. Peslherbe

124. Theoretical study on the roles of divalent metal ions in GTP hydrolysis. Y. Wang, J. R. Collins, S. K. Burt

125. Role of second sphere Zn2+ ligands in Aeromonas proteolytica aminopeptidase. P. Munih, M. L. Klein

126. Varying Lewis acidity in ionic liquids with new force field parameters. O. Acevedo, J. D. Evanseck

127. PDDG/PM3 and PDDG/MNDO: Extension to the halogens. I. Tubert-Brohman, C. Ruch Werneck Guimar‹es, M. P. Repasky, W. L. Jorgensen

128. Rational development of a lone pair inclusive force field. S. M. Tschampel, R. J. Woods

129. CH/p interactions between ethene and aromatic amino acids. A. T. Macias, A. D. MacKerell Jr.

130. Development of new CHARMM force field parameters for novel DNA bending agents. A. Loccisano, S. M. Firestine, J. D. Evanseck

131. DNA bending by unnatural guanine nucleotides. S. A. Mueller-Stein, S. M. Firestine, J. D. Evanseck

132. Molecular dynamics simulation of retinoic acid receptors/retinoids. A. M. Waligorski, W. S. Meng, J. D. Evanseck

133. Calculation of the binding affinity of b-secretase inhibitors using the linear interaction energy method. B. A. Tounge, C. H. Reynolds

134. Structure-based design of statine analogs as BACE1 inhibitors. K. Y. Fan, B. Hu, D. Cole, K. Bridges, R. Chopra, E. S. Manas, A. Katz, J. C. Alvarez, F. E. Lovering, P. Zhou, G. Jin, R. Cowling, J. Bard

135. Bioinformatics and structural bioinformatics analyses of galectin ligand binding specificities and its implication in developing target specific photodynamic therapy agents. T. Liu, T. Chu, M. Shibata, T. J. Dougherty, R. K. Pandey

136. Curariform antagonists bind in different orientations to acetylcholine binding protein. F. Gao, B. Nina, A. Little, H. Wang, S. M. Sine

137. Structure-based drug design using knowledge-based potentials. B. N. Dominy, E. I. Shakhnovich

138. Construction and simulation modeling of Mycobacterium tuberculosis cell walls. X. Hong, A. J. Hopfinger

139. Molecular modeling of intein structure. E. Storm, P. Biswas, S. Garde, G. Belfort

140. Comprehensive pharmacophore analysis: Application to HIV NNRTI. K. Torikoshi, S. Louise-May, G. Vigliotti, C. Marlor, D. Buechter, M. Deshpande, A. Agarwal

141. Combination of receptor-based and ligand-based drug design: Application in 3D-QSAR of HIV-1 RT non-nucleoside inhibitors. Z. Zhou, J. D. Madura

142. Validation of a model for the complex of HIV-1 reverse transcriptase with non-nucleoside inhibitor TMC125. M. Udier-Blagovic, J. Tirado-Rives, W. L. Jorgensen

143. Targeting the disruption of HIVgp41 mediated cell membrane fusion: Docking and MM-GB/PBSA studies. R. C. Rizzo, M. Gochin, I. D. Kuntz

144. Evaluation of strategies for molecular docking. D. Cheney, L. Mueller

145. Rescaling optimization: Applications to flexible ligand docking. E. D. Akten, J. Che

146. Enrichment of high-throughput docking results using naive Bayes. A. E. Klon, M. Glick, M. Thoma, P. Acklin, J. W. Davies

147. Molecular docking for generating peptides and peptido-mimetics inhibitors for thrombin and factor Xa. C. C. Clement, M. Philipp, J. Gingold

148. Optimization of DOCK for RNA targets. P. T. Downing, V. L. Thomas, T. L. James, I. D. Kuntz

149. Docking studies of peptide/HLA-A2.1 complexes. T. G. Kucukkal, W. S. Meng, J. D. Evanseck

150. Docking studies of the orphan nuclear receptor LRH-1: A potential target for tissue specific cancer therapy. T. Aynechi, H. A. Ingraham, I. D. Kuntz

151. Analysis of conformational families of analogs of GBR 12909. C. A. Venanzi, D. Pandit, M. Misra, K. M. Gilbert, D. Matecka, T. Prisinzano, K. C. Rice

152. Conformational analysis of methylphenidate. C. A. Venanzi, K. A. Paris, N. H. Naik, K. M. Gilbert, W. J. Skawinski, H. M. Deutsch

153. Application of a coarse-grained dynamical method to explore the conformational space of small molecules. Y. Wu, P. S. Hammond, T. J. Minehardt, J. D. Schmitt, R. Car

154. How the membrane retention of in vitro permeability affects precision/accuracy of in silico permeability prediction. S. Chong, L. Zhang, S. R. Johnson, T. R. Stouch

155. Molecular modeling of the chemokine receptor CCR5 and its small molecule antagonists as anti-AIDS therapeutics. M. Song, C. M. Breneman, N. Sukumar

156. Sodium channel design libraries from mining to novel compounds: A pharmacophore-based approach. T. B. Nguyen

157. Preliminary pharmacophore model for methylphenidate class of dopamine reuptake inhibitor. C. A. Venanzi, M. Misra, K. M. Gilbert, R. A. Buono, M. M. Schweri, Q. Shi, H. M. Deutsch

158. Computational modeling studies on anti tumor activity of bis-acridines against Murine P388 leukemia cells, Murine Lewis lung cells (LLc) and Human Jurkat leukemia wild-type cells(JLc): A graph theoretical approach. N. Sapre

159. Using a Kohonen self - organizing map to generate representative training, cross validation and prediction sets for QSAR modelling. R. Guha, J. R. Serra, P. C. Jurs

160. Study of SAR for 5-[bis(2chloroethyl)amino]-2-methyl-4-nitro(amino)-N-substituted imidazole using semiempirical calculation by Hyperchem Professional. I. Weidlich, S. Sobiak

161. Predicting the genotoxicity of polycyclic aromatic compounds from molecular structure with different classifiers. L. He, P. C. Jurs, L. Custer, S. K. Durham, G. M. Pearl

162. Combinatorial QSAR: Hunting for predictive models. P. de Cerqueira Lima, A. Kovatcheva, A. Golbraikh, Y. Xiao, S. Oloff, A. Tropsha

163. Principal curves analysis and self-organizing maps in QSAR: A comparative study. Y. Xiao, J. Klucik, R. Harris, J. D. Schmitt

164. An application of the QM-QSAR method to predict refractive index of the dental resin composite. A. J. Holder, L. Ye, J. D. Eick, C. Chappelow, P. Knox

165. Application of 3D-QSAR to the study of metallocene-based catalyst polymerization. V. L. Cruz, J. Ramos, A. Mu–oz-Escalona, J. Martinez-Salazar

166. Quantitative structure-based design: Formalism and application of receptor-dependent (RD) 4D-QSAR analysis to a set of glucose analog inhibitors of glycogen phosphorylase. D. Pan, Y. Tseng, A. J. Hopfinger

167. G protein-coupled receptors (GPCRs)-directed mining: A pharmacophore-based approach. T. B. Nguyen

168. Modeling transmembrane peptides. D. sengupta

169. Kinetic and thermodynamic aspects of recognition in a multiprotein environment. G. A. Papoian, P. G. Wolynes

170. Testing simple models of protein folding with computer simulation. L. L. Thomas, J. Pitera, J. Rice, J. D. Madura, W. Swope

171. Phi values and the folding transition state of protein G: Utilization and interpretation of experimental data through simulation. I. A. Hubner, J. Shimada, E. I. Shakhnovich

172. Energetic determinants of the structure of transmembrane helix dimers. M. Mottamal, J. Zhang, T. Lazaridis

173. Protein loop predictions using low barrier molecular dynamics. R. Geney, V. Hornak, C. Simmerling

174. Folding kinetics of a §-hairpin: A molecular dynamics study. A. Okur, D. R. Roe, G. Cui, V. Hornak, C. Simmerling

175. Analysis and prediction of the oligomeric state of coiled coils. J. Ramos, T. Lazaridis

176. Computer-aided prediction of new pharmacological actions in launched drugs. D. V. Akimov, D. A. Filimonov, V. V. Poroikov

WEDNESDAY MORNING
Section A
Javits Convention Center -- 1E11

The Challenge of Simulating Fluid Properties for Industry

R. D. Mountain, Organizer

8:00 — Introductory Remarks.

8:10 —177. Estimating thermodynamic properties for chemical process design. M. Schiller

9:00 —178. Towhee: A Monte Carlo molecular simulation program for industrial applications. M. G. Martin

9:50 — Intermission.

10:10 —179. Critical issues in the application of quantum chemistry in computational kinetics. C. A. Gonzalez

11:00 —180. Coupling detailed kinetics and transport. A. M. Dean, H. Carstensen, R. J. Kee, C. Sheng, K. M. Walters, H. Zhu

WEDNESDAY MORNING
Section B
Javits Convention Center -- 1E13

Structure Based Drug Design in Signal Transduction and Cell Cycle

Computational Studies of Signal Transduction and Protein Kinases I

E. Lunney and G. M. Verkhivker, Organizers

8:00 —181. Computational studies of molecular recognition: Applications to the binding specificity of signaling domains. B. Honig

8:35 —182. Phylogenomic studies of molecular signaling. O. Lichtarge

9:10 —183. Characterization of protein binding sites using computational solvent mapping. S. Vajda, M. Silberstein

9:45 — Intermission.

10:00 —184. Kinase binding and selective inhibitor design. W. L. Jorgensen, Y. Tominaga

10:35 —185. Structure-driven lead discovery and optimization. J. M. Blaney

11:10 —186. Multiscale simulations of protein kinase. Y. Zhang, Y. Cheng, J. A. McCammon

WEDNESDAY MORNING
Section C
Javits Convention Center -- 1E12

Computational and In Vitro ADME Data: What is it Worth and How to Use It?

Cosponsored with CINF
P. D. J. Grootenhuis, Presiding

8:00 —187. Role of predictive ADME and toxicity modeling in drug discovery. A. G. E. Wilson

8:45 —188. Structural alerts for hepatotoxicity. W. J. Egan

9:15 —189. Boosting the limits in early ADME prediction. M. Pintore, N. Piclin, H. van de Waterbeemd, J. R. Chretien

9:45 —190. Challenges in predictive ADMET: imperfect data in an imperfect world. S. R. Johnson

10:15 —191. Classifying the mutagenicity of two diverse sets of organic compounds using Ames test data for Salmonella typhimurium TA100 and TA98. B. E. Mattioni, P. C. Jurs, D. T. Stanton

10:45 —192. Development of an in silico predictive protocol for hERG liability. H. Wang, V. Madison, X. Zhang, S. Sorota

11:15 —193. Using targeted measurements to improve the accuracy of predictions of molecular physical properties. R. S. DeWitte, E. Kolovanov

11:45 —194. The failure of in vitro ADME properties to correctly determine in vivo outcomes. D. A. Norris, T. Bremer, K. Holme, G. Leesman, M. Sud

12:15 —195. Challenges for in silico modeling of ADME data. T. R. Stouch

Protein Families as Targets

Cosponsored with MEDI

Frontiers in Biophysical Methods

Novel Spectroscopies and Microscopies

Cosponsored with PHYS

WEDNESDAY AFTERNOON
Section A
Javits Convention Center -- 1E11

The Challenge of Simulating Fluid Properties for Industry

R. D. Mountain, Organizer

1:00 —196. Molecular modeling of the thermodynamic and transport properties of industrially-relevant fluids: Methods, results and insights. E. J. Maginn

1:50 —197. Molecular and mesoscopic simulations of phase equilibria. A. Z. Panagiotopoulos

2:40 — Intermission.

3:00 —198. Modeling chemical reactivity in fluids. B. Garrett

3:50 —199. Toward transferable, extensible, accurate and modularized force fields. H. Sun

WEDNESDAY AFTERNOON
Section B
Javits Convention Center -- 1E13

Structure Based Drug Design in Signal Transduction and Cell Cycle

Computational Studies of Signal Transduction and Protein Kinases II

E. Lunney and G. M. Verkhivker, Organizers

1:30 —200. Energy landscapes and signal transduction processes. P. G. Wolynes, G. A. Papoian

2:05 —201. Modeling of protein-protein complexes in structural genomics. I. A. Vakser, A. Tovchigrechko

2:40 —202. Effective potentials for protein-ligand binding and folding with thermodynamic constraints. R. M. Levy, E. Gallicchio, A. Felts, L. Zhang

3:15 — Intermission.

3:30 —203. Docking studies of protein-ligand interactions in kinases using multiple protein conformations and induced fit modeling. R. A. Friesner

4:05 —204. Modeling the interactions between protein kinases and their inhibitors. C. F. Wong, P. Sims, J. Kua, Y. Zhang, J. A. McCammon

4:40 —205. Combination of de novo methods of drug design, virtual focused combinatorial libraries, and in silico screening as a highly efficient tool for lead generation. P. A. Petukhov, E. A. Volpe, Y. Yin, R. I. Glazer, A. P. Kozikowski

WEDNESDAY AFTERNOON
Section C
Javits Convention Center -- 1E12

General Contributions

Data Mining

R. A. Wheeler and W. D. Cornell, Organizers

1:00 —206. A novel pattern recognition method and its application to drug discovery. M. Glick

1:25 —207. 3D atom-based alignment with hypermolecules. N. J. Richmond, P. Willett, R. D. Clark

1:50 —208. Investigations in shape clustering for lead hopping. N. E. MacCuish, J. D. MacCuish

2:15 —209. Dipeptide QSAR using topological representation of structure. L. H. Hall II, L. M. Hall, L. B. Kier, B. Spasov

2:40 —210. Development and applications of a Hansch substituent constant predictor. T. Chiu, S. So

3:05 — Intermission.

3:15 —211. Comparison of virtual screening programs. M. D. Cummings, R. L. DesJarlais, A. C. Gibbs, V. Mohan, E. P. Jaeger

3:40 —212. Optimizing the statistical significance of in vitro and in silico assays. R. S. DeWitte

4:05 —213. Ad-hoc searching and exploring of integrated databases and data sources. L. Jardine, A. Krassavine, A. Payne, S. Porter

4:30 —214. The extensible computational chemistry environment: A toolkit for theoretical chemistry. B. J. Palmer, G. D. Black, K. L. Schuchardt, E. R. Vorpagel

Frontiers in Biophysical Methods

Manipulation and Fluorescence of Single Biomolecules

Cosponsored with PHYS

THURSDAY MORNING
Section A
Javits Convention Center -- 1E11

The Challenge of Simulating Fluid Properties for Industry

R. D. Mountain, Organizer

8:00 —215. Predicting phase equilibria using transferable force fields. J. I. Siepmann, B. Chen, C. D. Wick, J. M. Stubbs, L. Zhang, L. Sun, X. S. Zhao

8:40 —216. Molecular modeling of nano-porous materials and confined fluids. K. E. Gubbins, R. J. -. Pellenq, J. Pikunic, F. R. Siperstein

9:20 —217. Calculation of excess thermodynamic properties using force field-based methods. D. Rigby

10:00 — Intermission.

10:20 —218. Molecular simulations of membrane based separation processes. S. Murad, W. Jia, M. Krishnamurthy

11:00 —219. Transferable force fields for thermophysical property simulation. J. F. Ely, H. Zhang

11:40 — Concluding Remarks.

THURSDAY MORNING
Section B
Javits Convention Center -- 1E13

Structure Based Drug Design in Signal Transduction and Cell Cycle

Proteomics and Chemical Genetics Approaches in Signal Transduction

E. Lunney and G. M. Verkhivker, Organizers

8:00 —220. Mechanistic insights into receptor-mediated cell signaling from computational and experimental probing of structure-function relations. H. Weinstein

8:35 —221. Signal transduction by JNK. R. J. Davis

9:10 —222. Activation of SR proteins by phosphorylation. J. Adams

9:45 — Intermission.

10:00 —223. Chemical genetic and proteomic approaches to the study of protein tyrosine phosphatases. Z. Zhang

10:35 —224. Chemical approaches to sorting out protein phosphorylation. P. A. Cole

11:10 —225. Chemical genetic approaches to study signal transduction. K. Shah, F. Vincent, S. Cook, S. Kim

THURSDAY MORNING
Section C
Javits Convention Center -- 1E12

General Contributions

R. A. Wheeler and W. D. Cornell, Organizers

8:00 —226. "Antifreeze" proteins at the ice/water interface. P. Dalal, J. E. Knickelbein, A. D. J. Haymet, J. D. Madura

8:20 —227. Novel variable transformation approach for enhancing conformational sampling in complex systems. P. Minary, G. Martyna, M. E. Tuckerman

8:40 —228. Efficient generation and characterization of low-energy folded states of a model protein: automated histogram filtering. S. A. Larrass, L. M. Pegram, H. L. Gordon, S. M. Rothstein

9:00 —229. Density of states simulation of proteins in a continuum. N. Rathore, J. J. de Pablo

9:20 —230. Proteins under stress: molecular simulation studies of pressure denaturation of proteins. S. Garde, A. E. Garcia, T. Ghosh

9:40 — Intermission.

9:50 —231. Two-phase thermodynamic method for accurate free energies for liquids directly from molecular dynamics simulations. S. Lin, M. Blanco, W. A. Goddard III

10:10 —232. Accurate calculations of absolute pKa values for substituted phenols in water with a polarizable force field. G. A. Kaminski

10:30 —233. Modeling metal affinitie as a function of intermolecular forces. M. Charton

10:50 —234. New formulation of non-equilibrium solvation and solvent effect of electron transfer. X. Li, K. Fu, Q. Zhu, M. Shan

11:10 —235. Self-energy of reaction field and solvation shift of spectra. K. Fu, Q. Zhu, X. Li, Z. Gong

Frontiers in Biophysical Methods

Structure and Dynamics of Transient Intermediates

Cosponsored with PHYS

THURSDAY AFTERNOON
Section A
Javits Convention Center -- 1E11

Structure Based Drug Design in Signal Transduction and Cell Cycle

Functional Role of Protein Kinases in Signal Transduction and Kinase Inhibitor Complexes

E. Lunney and G. M. Verkhivker, Organizers

1:00 —236. Information flow in MAP kinase pathways. M. H. Cobb, Z. Chen, M. Raman, B. Xu, B. Lee, L. Lenertz, T. Zhou, X. Min, S. Earnest, S. Stippec, E. J. G. Goldsmith

1:35 —237. Structural basis for protein recruitment to the activated insulin receptor. S. R. Hubbard

2:10 —238. Pharmacological inhibitors of cyclin-dependent kinases (CDKs) and glycogen synthase kinase -3 (GSK-3). L. Meijer

2:45 — Intermission.

3:00 —239. From consensus sequence to high affinity ligand: Acquisition of powerful inhibitors for signal transducing proteins. D. S. Lawrence

3:35 —240. Use of high-throughput nanovolume crystallization in structure-based drug design. J. A. Stafford

4:10 —241. Insights into AGC-kinase inhibitor binding from studies with PKA. D. Bossemeyer, M. Ga§el, C. B. Breitenlechner, S. Herrero de Vega, R. A. Engh

THURSDAY AFTERNOON
Section B
Javits Convention Center -- 1E13

General Contributions

Ligand Binding

J. D. Madura, Presiding
R. A. Wheeler and W. D. Cornell, Organizers

1:30 —242. An efficient conformational optimization method. J. Che, E. D. Akten

1:50 —243. Binding to an RNA aptamer changes the charge distribution and conformation of Malachite Green. T. Dieckmann, D. H. Nguyen, W. H. Fink

2:10 —244. Analysis of protein-sugar interactions. P. Dalal, L. L. Thomas, N. N. Aronson Jr., J. D. Madura

2:30 —245. Computational docking and opioidmimetics: Investigation of d-opioid agonist and antagonist receptor interactions. S. Bryant, L. H. Lazarus, S. Salvadori, R. Guerrini, G. Balboni, Y. Jinsmaa

2:50 — Intermission.

3:10 —246. Chemical genetics approaches to study signal transduction. K. Shah, F. Vincent, S. Cook, S. Kim

3:30 —247. Molecular modeling study of pyrazolopyrimidinone inhibitors of cyclin-dependent kinases. K. A. Rossi, J. A. Markwalder, S. P. Seitz, C. Chang, S. Cox, M. Boisclair, L. Brizuela, S. L. Brenner, P. Stouten

3:50 —248. Computational approaches to understand selectivity between estrogen receptors alpha and beta. R. J. Unwalla, E. S. Manas, C. P. Miller, Z. Zhang

THURSDAY AFTERNOON
Section C
Javits Convention Center -- 1E12

General Contributions

Quantum Chemistry

R. A. Wheeler and W. D. Cornell, Organizers

1:30 —249. Ab-Initio molecular dynamics with maximally localized Wannier functions. M. Sharma, R. Car

1:50 —250. Ab initio molecular dynamics study of the aqueous formate ion. K. Leung, S. B. Rempe

2:10 —251. Structures and dynamics of air-water interface from ab initio molecular dynamics. I. W. Kuo, D. J. Tobias, C. J. Mundy

2:30 —252. Vibrational spectra of 1-hexanol in n-hexane via ab initio molecular dynamics. J. M. Stubbs, J. I. Siepmann

2:50 — Intermission.

3:00 —253. A comparison of computed and observed Heats of Formation. J. J. P. Stewart

3:20 —254. Error correction of calculated Heat of Formation. L. H. Hu, X. Wang, L. H. Wong, G. H. Chen

3:40 —255. Novel linear scaling LocalSCF method for semiempirical quantum-chemical calculation of ultra-large bio-molecules. N. A. Anikin, V. M. Anisimov, V. L. Bugaenko, V. V. Bobrikov, A. M. Andreyev

4:00 —256. Semiempirical study of cationic polymerization reactions of monomer systems. A. J. Holder, M. D. Miller, J. D. Eick, C. Chappelow

4:20 —257. Design of a new familiy of molecules containing planar tetracoordinate carbons. A. Vela, G. Merino, M. A. Mendez-Rojas

Frontiers in Biophysical Methods

Structure and Dynamics of Transient Intermediates

Cosponsored with PHYS


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