The Computers in Chemistry Division
Spring 1999 ACS Meeting Program
Sunday Morning
Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR
4-D-QSAR analysis for virtual high-throughput screening, docking alignments, and hypothesis generation.
A.J. Hopfinger, P. Venkatarangan, S.Wang, A. Reaka, J. Duca
Applying ligand-docking technology to large datasets.
T.W. Heritage, S.N. Burkett, A. Nayeem R.D. Clark
In silico screening applied to the rational design of novel immunosuppressive compounds.
R. Lahana, A. Yasri, G. Grassy, B. Calas, M. Kaczorek, R. Buelow
Structure-based design of combinatorial libraries.
R.D. Brown, J. Jiang, P.D. Kirchoff, C.M. Venkatachalam
Conformational Analysis: Stepping Up to the New Challenges
Combinatorial libraries and structure-based design.
A.G. Skillman, I.D. Kuntz
Confort: A rational conformation analysis tool.
R. Balducci, R.S. Pearlman
Skizmo: A new program for rapid conformational analysis and structure-based design of combinatorial libraries.
W.P. Walters, M.T. Stahl, J.J. Corkery, M.A. Murcko
Conformational analysis: Finding the global minimum.
J.M. Leonard, A. Nayeem
Recent advances in rule-based conformational analysis.
K. Davies, M. Baird
Conformational analysis by intersection: Ring conformations.
A. Smellie, S.L. Teig
Using Computers to Facilitate Learning
Facilitating chemical education with computers: World Wide Web-based interactive materials and organizational tools for learning exercises.
A.L. Parrill, J. Ellsworth
Do World Wide Web-based practice quizzes improve student performance on exams?
J.H. Reeves, S. Broadway, C.R. Ward
Research methods in chemistry.
J.M. LoBue, J. Orvis
World Wide Web-based exercises for chemistry students using "live" molecular models.
H.G. Ungar, L. Calciano, A.E. Baucom, J.S. Lipscomb, J.N. Camara
TutOrg—an intelligent tutoring system: Application to bonding, resonance, and isomerism.
W.T. Wipke, J. Shoop, P. Madrid, J. Junker
Sunday Afternoon
Applications of Computational Chemistry to Toxicology and the Development of Agricultural Chemicals
Current trends in toxicology.
H. Salem
Computational investigations on the reaction of oximes with organophosphorus compounds.
J.B. Wright, W.P. Ashman, W.E. White
Theoretical study of the SNV reaction of trichloroethylene + CH3S- as a model for glutathione conjugation of TCE.
J-Y. Shim, P.F. Boon, A.M. Richard
Theoretical studies of DNA base deamination: The structure of "guanine diazonium ion" in its aggregate with cytosine.
R. Glaser, M. Lewis, S. Rayat
Regiochemistry of nucleic acid adduct formation via aryl nitrenium ion intermediates.
G.P. Ford
Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR
Designing large "smart" combinatorial libraries: Activity-based validations of diversity hypotheses.
D. Schnur
De novo design using HTS data.
K. Davies
Search techniques used in identifying actives in a large HTS dataset.
R.W. Spencer
Analyzing large datasets with decision trees: Discriminating between potential drugs and nondrugs.
M. Wagener, V. vanGeerestein
Conformational Analysis: Stepping Up to the New Challenges
Rapid conformation search applied to ligand discovery.
M.T. Stahl, A. Nicholls, R.A. Sayle, J.A. Grant
Implementation of fast conformational search strategi
Filtering techniques for 3-D database searching with catalyst pharmacophores.
R. Griffith, P.A. Keller, S. Leach
Alignment of 3-D structures by the method of 2-D projections.
P.D. Lyne, D.D. Robinson, W.G. Richards
Prediction of the bioactive conformation of arachidonyl ethanolamide using distance-constrained systematic search.
J-Y. Shim, W.J. Welsh, B. Berglund, A.C. Howlett, P.F. Fleming, K.C. Rice
Investigations into polysaccharide conformations via potential of mean force calculations.
K.J. Naidoo, M. Kuttel
Why dynamic simulations are necessar
Regular patterns followed by distributions of oligopeptide sequences among structural motifs.
S.G. Jacchieri
Using Computers to Facilitate Learning
Chemsite for nonmajors chemistry.
D.D. Shillady
Conservation laws and kinetic simulations.
S.L. Cooke
Interactive computer-based pedagogical tools.
M.A. McBrien, A.J. Williams
Learning biochemistry with highly interactive multimedia.
D. Mackay, J. Fetrow, A. Hagler
New approach to laboratory reporting.
B. Jacob, A. Fraiman
C-MoR chemistry project: Development of tools for visualizing chemical entities and chemical concepts.
R.N. Dominey, W.H. Myers, E.W. Goldman, R.P.F. Kanters
Monday Morning
Applications of Computational Chemistry to Toxicology and the Development of Agricultural Chemicals
Quantitative structure-activity relationship models useful for risk assessment in predicting suspected endocrine-disrupting compounds.
W.J. Welsh, S-J. Yu, Y. Chen, W. Tong, R. Perkins, D. Sheehan
Relationship of reactivity of organophosphorus compounds to toxicity.
W.E. White
Prediction of acute fathead minnow toxicity of organic compounds from molecular structure.
P.C. Jurs, D.V. Eldred, C.L. Weikel
Combined application of QSAR and database mining in search of environmental estrogens.
A. Tropsha, W. Zheng, J.D. McKinney
Prediction of rice blast activity using the electron-conformational method of identification of the pharmacophore and antipharmacophore shielding.
I.B. Bersuker, R.S. Pearlman, S. Bahceci, J.E. Boggs
Bridging the Gap Between Chemical Modeling and Engineering
From atomistic simulations to engineering models.
W.A. Goddard III, M. Blanco, T. Cagin, J. Sefcik, S. Hwang, Y. Jang, Y. Zhou
Computational chemistry and its use for process design.
D.A. Dixon
Quantum mechanics as a valuable partner in pilot-plant process development.
A.M. Chaka
interface of electronic structure theory and dynamics for the calculation of chemical reaction rate constants.
D.G. Truhlar, Y-Y. Chuang, J.C. Corchado, P. Fast, M.L. Radhakrishnan, J.M. Rodgers, M.L. Sanchez, J. Villa, B. Lynch, C.J. Cramer
Between chemistry and chemical engineering: Theoretical chemistry methods lead to reactor simulations.
H. Sellers, J. Gislason
From first-principles quantum chemistry to catalytic kinetics.
M. Neurock, P.S. Venkataraman, E.W. Hansen
Opportunities for quantum chemistry in chemical engineering.
J. Ruiz
Insights into NOx reduction catalysis from molecular modeling.
W.F. Schneider, K.C. Hass, B.R. Goodman, D. Sengupta, J.B. Adams
Acyl transfer mechanisms revisited: Computational mechanistics of anhydride alcoholysis.
P.M. Margl, B.E. Wilson
Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR
Dirty CoMFA, dirty docking, and a clean method for inverse QSAR-based drug design.
R.S. Pearlman, R. Balducci, K.M. Smith, M-Y. Brusniak
SPD: The generation of spacially resolved property descriptors.
C.E. Whitehead, C. Breneman
Parallel QSAR.
D.K. Agrafiotis, V.S. Lobanov, D.N.Rassokhin
Rapid generation of polarization-corrected electrostatic fields using the TAE/RECON method.
C.E. Whitehead, C. Breneman, D. Ryan
Monday Afternoon
Applications of Computational Chemistry to Toxicology and the Development of Agricultural Chemicals
Modeling interaction potentials as tools for understanding ligand-binding processes in chemical toxicity.
J. Rabinowitz, S.B. Little
Molecular dynamics simulations of tetracoordinate phosphonyl and carbonyl adducts of acetylcholinesterase.
I.M. Kovach, I.J. Enyedy
Ab initio structures of metalloenzyme active sites: Application to metalloglutathione transferase.
M. Krauss
Modeling dynamic chemical systems using cellular automata.
P.G. Seybold, L.B. Kier, C.K. Cheng
Application of computer modeling to toxicology.
R.S.H. Yang
Bridging the Gap Between Chemical Modeling and Engineering
Causes, consequences, and correctives for the gap in modeling between chemistry and chemical engineering.
S.W. Churchill
Chemical engineering applications of molecular simulation and computational chemistry.
P.T. Cummings
Computational materials design to address real world challenges.
A.M. Rappe
Physical property modeling: Some whys, whats, hows, and what-ifs.
J.P. O'Connell
Prediction of chemical properties of organic compounds using GA-CNN modeling of calculated structural descriptors.
P.C. Jurs, S.R. Johnson, H.L. Engelhardt, D.V. Eldred, G.A. Bakken, E.S. Goll
Reaction engineering of flame suppression: Integrating ab initio computations to flow/chemistry modeling.
M.R. Zachariah, D. Burgess, W. Tsang, P.R. Westmoreland
Molecular modeling applied to industrial chemical systems.
L.M. Bormann-Rochotte, J.T. Golab
Using molecular dynamics to design an effective corrosion barrier for a high-temperature superconductor.
C.A. Wells, J.E. Ritchie, J.T. McDevitt, D.R. Kanis
Structure-activity modeling methods in materials chemistry, materials formulations, and materials combinatorial chemistry.
M.J. Doyle
Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR
Binary QSAR: A new method for the determination of quantitative structure-activity relationships.
P. Labute
Combined recursive partitioning and fast conformation-generation methods for identifying pharmacophores from large chemical datasets.
X. Chen, A. Rusinko III, A. Tropsha, S.S. Young
Application of binary-QSAR to large combinatorial libraries.
D.L. Lynch, G. Lauri
Pharmacophore model generation from high-throughput screening datasets.
J.W. Elling, S.I. Bassett, R.F. Nutt
Monday Evening
Sci-Mix - EVE
Lateral validation of Hansch's models for Salmonella typhimurium determined by mutagenicity of nitroaromatics using Comfa.
R.L. Compadre, M. Fan, C. Byrd, C.M. Compadre
Toxic-substituted phenols in mainstream cigarette smoke condensate.
C.J. Smith, C. Hansch
NMR solution structure of the cons
Theoretical studies on the mechanism of electron transfer at the photosynthetic reaction center.
N. Miura, O. Kitao
Scampi: Statistical classification of activities of molecules for pharmacophore identification.
X. Chen, A. Rusinko III, A. Tropsha, S.S. Young
Structure of liquid clusters of Lennard-Jones atoms.
B.G. Moore, A.A. Al-Quraishi
Methodology for the optimization of chemical processes through statistical modeling with application on the nitration of bromobenzene.
A.C.R. Fabriani, E.A.N. Chrisman
Molecular modeling of polymer melts and blends.
J.D. Weinhold, J.G. Curro
Tuesday Morning
Bridging the Gap Between Chemical Modeling and Engineering
Molecular modeling of adsorption in amorphous nanoporous materials.
K.E. Gubbins, L.D. Gelb
Modeling the separation mechanism of oxygen-containing a
Molecular modeling and characterization of zeolites for sorptive separations.
B.K. Peterson
Atomistic simulations of boundry lubricant-bonding interactions with metal oxide surfaces.
S.M. Opalka, L.G. Hector Jr.
Modeling medium effects in condensed phases.
C.J. Cramer, J. Li, P.D. Winget, T. Zhu, D.G. Truhlar, D.A. Liotard
Functional mesoscopic dynamics of phase separation in complex copolymer liquids.
J.G.E. Fraaije, A.V. Zvelindovsky, G.J.A. Sevink, N.M. Maurits
Theoretical investigations of solute transport in liquid membranes containing photoactive carriers.
T.L. Longin
Modeling solvent effects on optical-limiting materials.
P.N. Day, K.A. Nguyen, R. Pachter
Multiscale modeling of structured materials.
D.B. Nicolaides, P. Kung
Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR
SACCS: Statistical analysis of combinatorial chemical sequences.
P. Shenkin
SAR information from screening data: Better than you would think.
G. Lauri
Some expectations of HTS.
J.J. Morris
Supervised GA-based regression clustering for data mining of molecular properties.
M. Embrechts, C. Breneman
High-throughput and combinatorial QSAR.
R.D. Clark
Corwin Hansch Award Symposium
QSAR, 3-D QSAR, and beyond.
H. Kubinyi, J. Sadowski
Have we made progress in predicting biological activity?
Y.C. Martin
Award Address (ACS Award for Computers in Chemical & Pharmaceutical Research). Demonstration of the use of a QSAR database to illustrate the development of a model for estrogenic toxicity.
C. Hansch
QSAR model for drug human oral bioavailability.
J.G. Topliss, F. Yoshida
Tuesday Afternoon
Bridging the Gap Between Chemical Modeling and Engineering
Chemistry to engineering: A bridge over troubled waters? Nah!
C.K. Hall
Infrastructure for quantum chemistry applications.
K.K. Irikura, R.D. Johnson III, C.A.Gonzalez, T.C. Allison, W.J. Stevens, C.B. Kellogg, U. Richter
Polymer modeling at Los Alamos: Atoms to continuum.
E.M. Kober
Force-field technology suitable for calculating thermodynamic parameters
of condensed phases.
J.M. Newsam, H. Sun, D. Rigby, B.E. Eichinger, A. Bick, C.M. Freeman, A.M. Gorman
Tales from the trail: Modeling polymerization catalysis.
A.K. Rappe
Critical issues in the steps to connect quantum calculations to bulk properties of glassy polymers.
P.J. Ludovice, S. Ahmed, J.V. Order, J. Jenkins
Developing polyhydroxamide as a low-flammability polymer: An interplay among computational chemistry, polymer synthesis and kinetics data.
P.R. Westmoreland, K. Rotem, T. Inguilizian, C. Gao, S.W. Kantor, R.E. Lyon
DMOL/COSMO-RS: A bridge between chemistry and chemical engineering.
N. Tanpipat, A. Klamt, I. Clausen, J. Andzelm
Calculation of acidities and basicities of silanols for reaction engineering of alkoxysilane
polycondensation.
J. Sefcik, W.A. Goddard III
Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR
Quick and dirty? No, fast and accurate: The K nearest-neighbor QSAR method.
A. Tropsha, W. Zheng, G. Ethiraj
Molecular descriptors for compound clustering.
H. Gao, J. Godden, J. Bajorath Convention
Development of a fingerprint to select training sets for predicting log P values.
S-Y. Yue, N. Tokinson, E. Roberts
Corwin Hansch Award Symposium
Calculating log P octanol: No missing fragments.
A.J. Leo
Structure-activity relationships for ligand-protein interactions: What can molecular dynamics simulations tell us?
P.A. Kollman
Recent success stories of classical QSAR procedure leading to (potentially) commercializable bioactive
compounds.
T. Fujita
Development of structure-activity relationships for assessing ecological risks.
S.P. Bradbury, G.D. Veith
Signposts along the road from classical QSAR to 3-D-QSAR to ??.
R.D. Cramer
Tuesday Evening
Poster Session
Comparative QSAR studies on anti-HIV HEPT derivatives.
R. Garg, C. Hansch
Utility of electron affinity as a QSAR descriptor in predictive toxicology.
S. Trohalaki, R. Pachter
Synthesis and structure-activity relationship of a series of 4-X-thiophenols. R.P. Verma, C.D. Selassie, S. Kapur, O.
Barberena, C. Hansch
Lateral validation of Hansch's models for Salmonella typhimurium determined by mutagenicity of nitroaromatics using Comfa.
R.L. Compadre, M. Fan, C. Byrd, C.M. Compadre
Measurements and prediction of log P values for highly lipophilic bioactive compounds.
C. Yamagami, T. Fujita
Use of computational techniques for predicting biodegradability of halogenated compounds by haloalkane dehalogenase.
B.T. Kawakami, P.V. Roberts
Comparative molecular field analysis of bisaromatic , -unsaturated ketone inhibitor of farnesyl protein transferase.
S-J. Yu, W.J. Welsh, N-D. Sung, M. Akamatsu, B-M. Kwon
Quantitative structure-activity relationship models for predicting the estrogenic activity of xenoestrogens.
S-J. Yu, W.J. Welsh, Y. Chen, W. Tong, R.
Perkins, D.M. Sheehan
Toxic-substituted phenols in mainstream cigarette smoke condensate.
C.J. Smith, C. Hansch
Amiloride binds to the more flexible sites on -DNA.
D.A. Bondarev, C.A. Venanzi
Influence of ligand binding on the dynamics of the M20 loop of DHFR and the implications for catalysis.
J.L. Radkiewicz, C.L. Brooks III
Normal-mode analysis of heme within myoglobin and related small molecules.
S.F. Sontum, I.I. Beraha, J.W. Dimmig, V.C.
Sundar
Standard force fields are not able to accurately model the energetics of very polar
compounds.
J.J. Harr, R.B. Shirts
Structural model for tubulin polymerization inhibition by colchicine site agents: A 3-D quantitative structure-activity relationship study.
Y. Fan, S-J. Zhang, S. Holden, J.B. Partridge,
N-S. Shen, T-N. Huang
NMR solution structure of the conserved 790 loop of 16S RRNA.
S. Varma, S. SantaLucia Jr.
Molecular modeling of the inhibition of mitochondrial malate dehydrogenase by cyclic AMP.
D.G. Harris, S. ScottZimmerman
Theoretical studies on the mechanism of electron transfer at the photosynthetic reaction center.
N. Miura, O. Kitao
Novel class of molecular shape descriptors and a method for validation of chemical diversity.
J. Liang
Optimizing small combinatorial libraries using a genetic algorithm.
D.J. Gordon, E.M. Bellott, B. Tenenbaum
Nonparametric analysis and design
of heteropolymer libraries. P. Constans, J.D. Hirst
Generation of isomers of organic molecules using genetic algorithms.
Q. Hui, W. Cai, M. Zhang
TheRate: A web-based tool for modeling kinetics of gas-phase reactions.
T.N. Truong, W.T. Duncan
Cerius2-SDK: A foundation for rapid local simulation software development.
M.A. VanDaelen, M.G. Peeler, S.D. Kahn
Scampi: Statistical classification of activities of molecules for pharmacophore identification.
X. Chen, A. Rusinko III, A. Tropsha, S.S. Young
Quantitative structure-activity relationships of RGD mimetics as fibrinogen-receptor antagonists.
M. Akamatsu, M. Miyashita, Y. Nakagawa, Y. Hayashi, Y. Sato, T. Fujita, T. Ueno
3-D-QSAR studies of taxoids and analogs.
M.A. Avery, J.B. Bhonsle, J.R. Woolfrey, J.K. Buolamwini, T. Mineno
Comparative molecular-field analysis 3-D-QSAR study of conformationally restricted cinnamyl HIV integrase inhibitors.
J.K. Buolamwini
Hologram QSAR of artemisinin analogs.
J.R. Woolfrey, C.R. Rodriges, M.Alvim-Gaston, E.J. Barreiro, F.E. Cohen, M.A.
Avery
3-D QSAR of peroxidic antimalarials based on artemisinin.
M.A. Avery, M. Alvim-Gaston, J.R. Woolfrey
3-D pharmacophore models of antimalarial drugs.
O.O. Clement, S.M. Efange
3-D QSAR of cyclic urea derivative as HIV-1 protease inhibitors.
A.K. Debnath
3-D QSAR of D4 antagonists based on full conformational searches and quantum
mechanically derived descriptors. M. Hennemann, T. Clark, H. Lanig
Quantum mechanical estimation of pK(HB).
M. Hennemann, T. Clark
Quantum mechanical and molecular mechanical modeling of enzyme-substrate interactions in alanine racemase.
M.J. Ondrechen, J.M. Briggs
Computational study of anomeric effects, stereoelectroni effects, and conformational energies of 2-substituted tetrahydro-2H-pyrans.
M.L. Kasner, F. Freeman, W.J. Hehre
Quantum chemical analysis of para-substitution effects on the electronic structure of phenylnitrenium ions in the gas phase and aqueous solution.
M.B. Sullivan, K. Brown, C.J. Cramer, D.G. Truhlar
Predicting NMR shielding by alkenes based on ab initio GIAO calculations.
N.H. Martin, N.W. Allen III, S.T. Ingrassia, E.K. Minga, J.D. Brown
Molecular mechanics (MM3) force-field development for tetravalent boron-containing compounds.
T.A. Holme, L.S. Fisher
Use of hexahydropyridobenzodioxins to examine the ability of molecular orbital methods to model hydrogen bonding.
W.H. Shelver, W.L. Shelver, K. Gholami
Low-barrier hydrogen bonds: Substituent effects on strength and geometry.
G.A. Kumar, M.A. McAllister
Solvation effect on stability of E/Z conformers of methyl acetate and its enolate anion: Ab initio combined QM/MM simulations.
K. Byun, J. Gao
Calibration of model core potentials: Application to the group 4 transition-metal halogen complexes.
S.A. Decker, M. Klobukowski, Y. Sakai, E. Miyoshi
Structure of liquid clusters of Lennard-Jones atoms.
B.G. Moore, A.A. Al-Quraishi
Computational methods for conformational analysis of unsymmetrical 1,3-diamines: 3-Aminotropanes.
J.B. Sorensen, A.H. Lewin, J.A. Dustman, J.P. Bowen
Computational study of organotellurium compounds.
H.N. Po, F. Freeman, W.J. Hehre
Paper 155: Reaction-class dynamical approach for modeling kinetics of gas-phase reactions.
D.K. Maity, T.N. Truong
Model potential of methane based on CCSD(T) calculations of methane dimers.
S. Tsuzuki, T. Uchimaru, M. Mikami, K. Tanabe
New tool for comparing vibrations of similar molecules and its application to models for the cysteine-linked tyrosyl radical from galactose oxidase.
R.A. Wheeler, K.E. Wise
Ab initio optimized geometric parameters for the 1,2-dinucleotide adducts of cisplatin.
F.H. Hausheer, P. Seetharamulu, S. Yao, J.D. Saxe, D. Reddy, K. Haridas, D. Murali, M. Zhao, P.N.V. Petluru
Recent developments in modeling nonlinear optical properties of inorganic complexes.
T. Zhou, T.R. Cundari, H.A. Kurtz
Applying ab initio methods toward improved protein circular dichroism calculations.
J.D. Hirst, N.A. Besley
Paper 161: Structure and energetics of Gd(III) interactions with water and ammonia.
E.D. Glendening, P.A. Petillo
Paper 162: Theoretical study of microscopic solvation of LiCl in water clusters: LiCl(H2O)n,
n=1–4.
D.E. Bacelo
Interaction of methanol with zeolitic petrochemical catalysts: A new ab initio embedded cluster study.
P. Treesukol, J. Vollmer, T.N. Truong, T. Limtrakul
Methodology for the optimization of chemical processes through statistical modeling with application on the nitration of bromobenzene.
A.C.R. Fabriani, E.A.N. Chrisman
Binding of divalent ligand to polyelectrolyte: A novel method to calculate the binding free energy and the salt dependence of free energy.
H. Ni, C. Anderson, M.T. Record, C.F. Charles
Parameterization and application of a generalized born model for proteins and nucleic acids.
B.N. Dominy, C.L. Brooks III
Modeling intermediate Q in the catalytic cycle of methane monooxygenase (MNO).
L.M. Thomson, M.B. Hall
Electronic structure and spectra of the ground and excited states of potential optical-limiting materials.
K.A. Nguyen, P.N. Day, R. Pachter
O(3P) reactions with alkanes (n=2–5), C2H5F, C2F6, C2F5Cl, and PHC2H5: A computational study of reaction mechanisms.
A. Gindulyte
Improved heats of formation from DFT calculations and an empirical group increment scheme.
L.R. Schmitz, N.L. Allinger, M. Chen, J. Labanowski
Molecular modeling of polymer melts and blends.
J.D. Weinhold, J.G. Curro
Wednesday Morning
Bridging the Gap Between Chemical Modeling and Engineering
Predicting thermophysical properties of multicomponent mixtures from
molecular simulations.
J.I. Siepmann, M.G. Martin, B. Chen, N.D. Zhuravlev, C. Wick
General approach for molecular simulation of phase equilibria in complex mixtures.
F.A. Escobedo
Molecular simulation of phase equilibria of 1-olefin systems.
I.G. Economou, T. Spyriouni, D.N. Theodorou
Methodologies for predicting thermal rate constants of gas-phase reactions.
T.N. Truong, W.T. Duncan
Improved calculation of bond dissociation energies of organic compounds based on the concept of stabilization energy.
E.A. Castro, M. Firpo, L. Gavernet
Hydrogen peroxide dissociation in supercritical water.
N. Akiya, P.E. Savage
New concept for the application of linear free-energy relationships in catalysis.
M.M. Ramírez-Corredores, I. Machín, M.E. Grillo
Using computational approaches to model hematite surfaces.
I. Lado-Touriño, F. Tsobnang, P. Ngoepe
Combinatorial Chemistry
Comparing methods of diversity selection for combinatorial chemistry and screening selection.
J.P. Holland, T.J. Mitchell
Paper 181: Rational selections from virtual libraries.
V.S. Lobanov, D.K. Agrafiotis, D.N. Rassokhin
Recent applications of ChemSpace shape similarity searching.
R.D. Cramer, M.A. Poss, M.A. Hermsmeier, T. Caulfield, M. Kowala
Leveraging HTS results to improve compound selection strategies.
M.G. Bures, Y.C. Martin
Paper 184: Diversity sampling: Selection, space coverage, and
visualization.
A. Tropsha, W. Zheng, G. Ethiraj, C.H. Reynolds, R. Druker, L.B. Pfahler, S.J. Chakravorty, T. Schlick, D. Xie
Evaluation of reagent-based and product-based strategies in the design of combinatorial libraries.
E.A. Jamois
Physical, Chemical, and Biological Property Prediction
Property prediction by combined simulation and QSAR/QSPR analysis.
A.J. Hopfinger, A. Kulkami, J.S. Duca
Density functional theory of spin-coupled diiron centers: -oxo-bis(-acetato) and -hydroxo-bis(-acetato) bridged models for diiron-oxo proteins.
J.K. McCusker, J.H. Rodriguez
Mathematical programming approach to DHFR inhibitor drug design.
A.K. Karalapakkam, L.E.K. Achenie
Prediction of physicochemical properties using a structure-fragment approach.
E.A. Kolovanov
Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena.
D.E. Clark
Wednesday Afternoon
Combinatorial Chemistry
Novel algorithms for the design of diverse and focused combinatorial libraries.
R.S. Pearlman, K.M. Smith
Sensitivity analysis and other tools for combinatorial library design.
E.J. Martin, A.K. Wong, J.M. Blaney, J.M. Hoeffel, J.M. Jansen
New developments in molecular diversity, similarity, and library design using both ligand and protein target-based information.
D.L. Cheney, J.S. Mason, B.R. Beno
Design of maximum information libraries as a highly efficient tool for lead generation: Theory and methods.
P. Beroza, R. Feinstein, J. Greene, B. Goldman, J.A. Mount, A. Smellie
Design of maximum information libraries as a highly efficient tool for lead generation: Application of the method.
E.K. Bradley, P. Beroza, J. Eksterowicz, H. Genin, P. Grootenhuis, D. Miller, J. Miller, J. Penzotti, W. Shirley, D. Spellmeyer, J. Srinivasan, R. Stanton
Search techniques used in identifying actives in a large HTS dataset.
P. Labute
Ligand Design and Biological Problems
Ligand docking for structure-based drug design.
X. Jiang, C.M. Venkatachalam, T. Oldfield, M. Waldman
Comparison of various docking strategies.
D. Joseph-McCarthy, B. Thomas, J.C. Alvarez
Design and synthesis of PDGFR-selective inhibitors.
C. Liang, C. Sun, G. McMahon, C. Tang
Computational approaches to ligand design against polymorphic targets.
R.J. Zauhar, G. Moyna, W.J. Welsh
Insights into -hairpin formation and stability from molecular dynamics simulation of short peptide folding.
H. Wang, S.S. Sung
Spontaneous base flipping in DNA.
Y-C. Chen, V. Mohan, R.H. Griffey
Physical, Chemical, and Biological Property Prediction
Estimation of gas-liquid critical properties.
A.N. Burgess, M.H. Barley, D. McCaughy
Prediction of liquid-crystal clearing temperatures from molecular structure.
P.C. Jurs, S.R. Johnson
3-D information-rich databases derived from quantum-mechanical calculations.
B. Beck, T. Clark, A. Horn, J. Carpenter
Molecular structure description: The electrotopological state.
L.H. Hall, L.B. Kier
Electrotopological state: Use in similarity and database management.
L.B. Kier, L.H. Hall
Thursday Morning
Combinatorial Chemistry
Structure-based library design: Application of new systematic protein-active site pharmacophore analysis.
I. Morize
Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase.
B. Shoichet, D. Tondi, U. Slomczynska, S. Ghelli, M. PaolaCosti, D.M. Watterson
Use of de novo structure-based design methods to focus combinatorial libraries.
E. Evensen, D. Joseph-McCarthy, G.A. Weiss, S.L. Schreiber, M. Karplus
Discovery of novel serine protease inhibitors by structure-based computational screening of virtual combinatorial libraries.
J.W. Liebeschuetz
Structure-based approaches to the design of combinatorial libraries.
J.H. VanDrie
Structure-based selection of combinatorial library subsets.
P. Johnson, A. Leach, J-F. Marchaland, Z. Szabo, M. Vargyas
General
Ab initio optimized geometric parameters for the DNA-base adducts of cisplatin.
P.N.V. Petluru, P. Seetharamulu, S. Yao, D. Reddy, K. Haridas, D. Murali, M. Zhao, F.H. Hausheer, J.D. Saxe
Effecient development of molecular mechanics parameters for transition metals.
W. Fu, T.R. Cundari
Classical conformational analysis to the max: Energy surfaces for disaccharides.
A.D. French, G.P. Johnson, M.K. Dowd, A-M. Kelterer
Canonical and Gibbs ensemble Monte Carlo simulations for systems with adiabatic separation of nuclear and electronic degrees of freedom.
B. Chen, J.I. Siepmann
IR and Raman spectra of bicyclic molecules using scaled correlated and noncorrelated force fields.
W.B. Collier, I. Magdo, T.D. Klots
Limitations of coupled cluster theory in predicting atomization energies.
D.F. Feller, K.A. Peterson
Physical, Chemical, and Biological Property Prediction
Using molecular hologram to predict n-octanol/water partition coefficient.
S-Y. Yue, N. Tomkinson, E. Roberts
Modeling partitioning phenomena with CM2-charge-based models for medium effects.
C.J. Cramer, J. Li, P.D. Winget, T. Zhu, D.G. Truhlar
Accurate prediction of solvation free energy and lipophilicity of organic molecules using atomic constants and fingerprints.
V.N. Viswanadhan, A.K. Ghose, U.C. Singh, J.J. Wendolowski
Modeling molecular interactions.
L.Y. Wilson, G.R. Famini
Use of quantum mechanics for QSPR and QSAR models with error estimation.
T. Clark, B. Beck, M. Breindl, M. Hennemann
Using the TLSER to investigate Henry's law constant and related properties.
G.R. Famini, D. Benyamin, C. Kim, R. Veerawat, L.Y. Wilson
Thursday Afternoon
Combinatorial Chemistry
Knowledge-based approach in designing combinatorial and medicinal chemistry libraries for drug discovery: 1.Qualitative and quantitative definitions of a druglike molecule.
A.K. Ghose, V.N. Viswanadhan, J.J. Wendolowski
Knowledge-based approach in designing combinatorial and medicinal chemistry libraries for drug discovery: 2. The design of a druglike library.
V.N. Viswanadhan, A.K. Ghose, A. Kiselyov, L. Smith, G. Rishton, J.J. Wendolowski
Chemsymphony: Java tools for handling diverse data in combinatorial chemistry.
P. Tebbutt, A. Krassavine, A. Hodgkin
NMR prediction software and tubeless NMR: An analytical tool for screening of combinatorial libraries.
A. Williams
General
Application of calibration transforming matrix method in simultaneous determination of tetradic mixtures of aromatic compounds using ultraspectrophotometry.
Q. Hui, W. Cai, M. Zhang
Adsorption of oxygen on reduced copper chromite catalyst.
R.A. Stowe, D.A. Hucul, R.K. Helling
Road to ammonium nitrate.
K.A. Mort, R.A. Jackson, P.J. Wilde
Physical, Chemical, and Biological Property Prediction
Using progressive scrambling to validate regression models.
R.D. Clark, J.M. Leonard
Prediction of molecular properties from momentum-space wavefunctions.
M.J. Sykes, E.F. McCoy
Empirically corrected ab initio thermochemistry.
K.K. Irikura, X. Wang
Linear-scaling
localized-density-matrix method and its applications.
G. Chen, S. Yokojima, W. Liang, D. Zhou, X. Wang
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