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The Computers in Chemistry Division
Fall 1999 ACS Meeting Program

Sunday Morning

Bioenergetics

Retinal's photoisomerization in bacteriorhodopsin.
F. Molnar, M. Ben-Nun, J. Baudry, T.J. Martínez, K. Schulten

Structure and thermodynamics in bacteriorhodopsin.
J.C. Smith, J. Baudry, S. Crouzy, B. Roux

Simulating energy flow in tuna cytochrome c after electron transfer.
Q. Wang, C.F. Wong, H. Rabitz, J.A. McCammon

Docking and Scoring

Protein-ligand binding and lead optimization via Monte Carlo simulations.
W.L. Jorgensen, J. Tirado-Rives

Hierarchical algorithm for rapidly docking ligands into a protein-binding site using a grid-based scoring function.
R.A. Friesner

Prediction of free energy of binding for charged ligands using the linear response approximation method.
L.S. Narasimhan, C.J. Blankley, C. Humblet, M. Snow

Computation and visualization of protein-ligand binding interactions.
E.O. Purisima, V. Vasilyev, T. Sulea

Nonlinear Optical and Electronic Materials

Atomic-scale modeling of electroactive materials: Investigation of contemporary and next-generation devices.
R.D. Pugh

Multimillion-atom molecular dynamics simulation of nanostructured materials on parallel computers.
R.K. Kalia

CI expansions for electronic g-tensor calculations: Applications to semiconductor defects.
G.H. Lushington

What is the resistance of a molecule?
S. Datta

Polymer ionization energies and electron affinities: Polyacetylene.
D.S. Dudis, A.T. Yeates

Electron transfer in dentritic macromolecules.
T.S. Elicker, D.G. Evans

Sunday Afternoon

Bioenergetics

How does nitrogenase work?
D.N. Beratan, I.V. Kurnikov

Studies on the initial photochemical event in photosynthetic systems.
M.C. Zerner

Nuclear dynamics and electronic transition in a photosynthetic reaction center.
M. Marchi, M. Souaille, M. Ceccarelli

Docking and Scoring

Approaches to describe and predict protein-ligand interactions.
G. Klebe, M. Hendlich, H. Gohlke

Working toward a consensus-scoring function.
R. Clark, A. Strizhev, A. Nayeem

Evaluation of scoring functions for protein-ligand docking.
W.P. Walters, P.S. Charifson, J.J. Corkery, M.A. Murcko

Pro_leads: A new approach to molecular docking and its application in screening compound libraries.
C.A. Baxter, C.W. Murray, B. Waszkowycz, J. Li

Nonlinear Optical and Electronic Materials

Nonvolatile memory application using mobile protons in the gate oxide.
K. Vanheusden, R.A.B. Devine, D.M. Fleetwood, W.L. Warren

Hydrogen in metal-oxide semiconductors.

Isotope effect in hot electron transistor degradation by hydrogen desorption.
B. Tuttle, K. Hess

Simulating atomic-scale processes in silica.
D.R. Hamann

Point defects in silcon dioxide and silicon nitride.
G. Pacchioni

First-principles study of oxygen deficient defects in silicate and germanosilicate glasses.
K. Raghavachari

Effect of charge trapping on the microscopic structure of oxygen vacancy centers in amorphous SiO2.
A.C. Pineda, S.P. Karna

Monday Morning

Celebrating the 25th Anniversary of the Division of Computers in Chemistry

When COMP was created and how and why.
P. Lykos

Chemical structures and chemical reactions using computers.
T. Wipke

Some call the world a dreary place.
R.E. Dessy

Historical review of molecular modeling.
B. Gelin

Nonlinear Optical and Electronic Materials

Novel organic photorefractive structures with high gain and fast-response time.
S. Bartkiewicz, A. Miniewicz, F. Kajzar, M. Zagorska

From fundamentals of two-photon processes to cellular mechanism of chemotherapy to 3-D memory.
P.N. Prasad, A. Schally, C. Liebow, A.A. Nagy, H. Pudavar, X. Wang, L.J. Krebs, J. Swiatkewicz, B.A. Reinhardt, C. Chong, K.S. Kim, T.C. Lin

Structure-property relationships of two-photon absorbing heterocyclic aromatic dyes.
J.W. Baur, M.D. Alexander Jr., B.A. Reinhardt, R.A. Vaia, S.M. Kirkpatrick, R. Kannan

Density functional theory for NLO: Success or failure?
R.J. Bartlett, C. Hirata, C. Jamorski, S. Ivanov

Trends and perspectives in electric hyperpolarizability calculations.
G. Maroulis

On the importance of the vibrational contributions to the hyperpolarizabilities of conjugated organic materials.
B.R. Champagne

Monday Afternoon

Celebrating the 25th Anniversary of the Division of Computers in Chemistry

From pen-and-ink to Star Trek and beyond: Some personal reflections on five decades in molecular graphics.
R. Langridge

Education with molecular modeling: Quantum chemistry for the masses.
W.J. Hehre

Review of semiempirical codes and their impact.
J.J.P. Stewart

Computer-aided drug discovery: Impact on human health, computing, and commerce.
P. Gund

Chemistry and the Internet: Perspectives on the future.
S.M. Bachrach

Nonlinear Optical and Electronic Materials

Conjugated molecules with large two-photon cross sections.
J.W. Perry, S.P. Ananthavel, S.M. Kuebler, S.R. Marder, M. Rumi, D.L. Dyer, M.D. Levin, D. McCord-Maughon, H. Röckel, B.H. Cumpston, A.A. Heikal, J.E. Ehrlich, D. Beljonne, T. Kogej, J-L. Brédas

Design of organic conjugated chromophores with large two-photon absorption cross sections.
D. Beljonne, J-L. Brédas

"Sum over state" revisited.
H. Sekino

Calculations on the electroluminescent properties of lanthanide-doped materials.
M.C. Zerner, T. O'Brien

Novel methods for color-tuning in organic LEDs.
M.E. Thompson, S.R. Forrest, P.E. Burrows

Organic light-emitting diodes: Exciton motion and control mechanisms.
M.A. Ratner

Monday Evening

SciMix

Crystallographic evidence for a strong sulfur-aromatic interaction.
R.J. Zauhar, C.L. Colbert, R.S. Morgan, W.J. Welsh

Ab initio derived force field for biomolecular applications with explicit treatment of electrostatic polarizability.
G.A. Kaminski, H.A. Stern, J.L. Banks, R. Zhou, R.A. Friesner, B.J. Berne

Scoring index to evaluate docked structures of peptide-protein complexes.
R. Casadio, I. Rossi, E. Arnofi, P. Fariselli

Calculated inhibitor-enzyme binding affinities and 3-D-QSAR comparative molecular-field analysis (CoMFA) studies on a series of Ritonavir (ABT-538) analogs as HIV-1 protease inhibitors.
P. Jayatilleke, A.C. Nair, R. Zauhar, W.J. Welsh

Coenzyme B12 chemistry: Insights from a computational study.
M. Torrent, D.G. Musaev, S-C. Ke, K. Warncke, K. Morokuma

Using the effective fragment-potential model to study the solvation of acetic and formic acids.
M.A. Freitag, M.S. Gordon

Use of the CURES-EC method in calculating electron affinities of triatomic molecules.
E.C.M. Chen, D.J. Hays, H. Allen

Ab initio study of the adsorption of MNA on H-terminated Si(100) surface modeled by SimHn clusters.
S.M. Black, C. Sapp-Mobley

Electronic structure studies of group 3-5 clusters.
P.P. Korambath, S.P. Karna

Are fullerenes and carbon nanotubes viable candidates for h6 metal ligands?
S.K. Goh, D.S. Marynick

Tuesday Morning

Bioenergetics

Toward ab initio theory of electron-transfer reactions in proteins.
A. Stuchebrukhov

Electron tunneling in proteins: Beyond the Pathways Model.
J.N. Onuchic, I. Balabin

Energetics of the electron transfer from Qa to Qb for the light and dark adapted reaction centers.
E.W. Knapp, B. Rabenstein, M.G. Ullmann

Structural, thermochemical, and binding properties of quinones and their anions in the photosynthetic reaction center of Rhodobacter sphaeroides.
R.A. Wheeler

Bridging the Gap: Theoretical Chemistry to Drug Design

Computational chemistry and drug design methods: What to teach and what not to teach?
J.P. Bowen

QSAR and drug design: Perspectives from industry and academia.
G.B. McGaughey

From a government lab to the pharmaceutical industry: Perspectives and experiences.
M.S. Head

Here be monsters: Pitfalls for the new computational chemist.
A.J. Holder

Docking and Scoring

Virtual "SAR by NMR."
P.W. Rose, B.A. Luty, L. Schaffer, T.J. Marrone

Incorporating flexibility, solvation, and molecular diversity in ligand screening.
L.A. Kuhn, V. Schnecke

Protein-ligand docking with a knowledge-based scoring function.
I. Muegge

Simulating affinity fingerprints: Statistical relationships among docking scores for different protein-binding sites.
R.T. Koehler, H.O. Villar

Nonlinear Optical and Electronic Materials

Reliable predictor of dopant activity in zinc blende semiconductors: Theory.
D.J. Chadi

Doping and growth of group 3 nitrides
J. Neugebauer, C.G. VandeWalle

Disorder effects in the electronic response of an array of quantum dots.
F. Remacle

Hartree-Fock cluster procedure for electronic structures and associated properties of solid-state systems and large molecules.
T.P. Das

Local and global bonding at the Si-SiO2 interface.
S.T. Pantelides, R. Buczko, M. Ramamoorthy, G. Duscher, S.J. Pennycook

Theoretical study of the microscopic structure and nonlinear optical properties of radiation-induced defects in a-SiO2.
A.M. Ferreira, H.A. Kurtz, S.P. Karna

Tuesday Afternoon

Bioenergetics

Theory of dissociative proton-coupled electron-transfer reactions.
R.I. Cukier

Theoretical studies of the Grotthuss mechanism in membrane proteins.
R. Pomès

Simulating proton translocations in proteins: Probing proton transfer pathways in the Rhodobacter sphaeroides reaction center.
A. Warshel, Y.Y. Sham, I. Muegge

Bridging the Gap: Theoretical Chemistry to Drug Design

Balancing the needs of the recruiters and the aims of the educators.
W.A. Warr

What I wish I knew then ... and sort of know now.
D.S. Hartsough

What skills do computational chemists need to make them effective at computer-assisted drug design in an industrial environment?
M. Cory

Modeling ADME parameters of a drug.
R.J. Vaz

Excited-state career transitions between computational chemistry and informatics: A personal perspective.
W.E. Reiher III

Docking and Scoring

Prediction of ligand-binding modes via energy-based genetic algorithm docking.
G.P. Brady Jr.

Docking strategies that account for ligand flexibility.
D. Joseph-McCarthy, B.E. Thomas IV, J.C. Alvarez

Surface signatures: A new approach for fast database docking.
R.J. Zauhar, W.J. Welsh, G. Moyna

Free energy functions for protein discrimination and docking.
S. Vajda, C.J. Camacho, R.S. Kimura, S. Dennis

Docking studies of salicylhydrazine inhibitors to the HIV-1 integrase catalytic domain.
A.L. Parrill, G.B. Ray

Nonlinear Optical and Electronic Materials

Mechanism of ultrafast nonlinear optical response in organic molecular materials studied by experimental observation and theoretical calculation.

Nonlinear absorption spectra of transparent organic materials (molecules, crystals, and nanocrystals): A comprehensive experimental and theoretical study.
P.L. Baldeck

Low-melting, mixed organic-inorganic salts as nonlinear optical materials.
J.S. Wilkes, A.T. Yeates

Quantum and semiclassical modeling of solvent effects on NLO properties.
H. Agren

Medium effects on molecular nonlinear optical properties: Theory and applications in the polarizable continuum model.
R. Cammi, B. Mennucci, J. Tomasi

Computational approaches toward the nonlinear optical properties of conjugated organic polymers in the solid-state.
B. Kirtman

Tuesday Evening

Poster Session

Comparative molecular field analysis on cyclic urea compounds as HIV-1 protease inhibitors.
X. Wang, W.J. Welsh

Crystallographic evidence for a strong sulfur-aromatic interaction.
R.J. Zauhar, C.L. Colbert, R.S. Morgan, W.J. Welsh

Design and synthesis of diboronic acids: Reversible inhibitors of cathepsin B for the therapeutic treatment of cancer.
S. Puri, G.D. Duncan, W.J. Welsh

Discovery of novel inhibitors of the papillomavirus E6 protein mediated p53 degradation by 3-D database searching.
J.H. Voigt, E.J. Androphy, J.J. Chen, M.C. Nicklaus, J.D. Baleja

Molecular modeling of HIV protease inhibitors.
C. Parish, T. Lyons

3-D molecular determinants of estrogen-receptor isoforms.
A. Bhat, R. Abagyan

Ab initio derived force field for biomolecular applications with explicit treatment of electrostatic polarizability.
G.A. Kaminski, H.A. Stern, J.L. Banks, R. Zhou, R.A. Friesner, B.J. Berne

Scoring index to evaluate docked structures of peptide-protein complexes.
R. Casadio, I. Rossi, E. Arnofi, P. Fariselli

Prediction of the binding site of paclitaxel, epothilone, and discodermolide on tubulin by docking studies.
J.B. Bhonsle, M.A. Avery

Generating a model of the protein-ligand complex of p56lck tyrosine kinase SH2 domain and an oxamic acid dipeptide (a nonhydrolysable, monocharged phosphate replacement).
D.R. Cameron, P.L. Beaulieu, J-M. Ferland, J. Gauthier, E. Ghiro, J. Gillard, V. Gorys, M. Poirier, J. Rancourt, D. Wernic, M. Llinàs-Brunet, R. Betageri, M. Cardozo, E.R. Hickey, R. Ingraham, S. Jakes, A. Kabcenell, T. Kirrane, S. Lukas, U. Patel, J. Proudfoot, R. Sharma, L. Tong, N. Moss

Calculated inhibitor-enzyme binding affinities and 3-D-QSAR comparative molecular-field analysis (CoMFA) studies on a series of Ritonavir (ABT-538) analogs as HIV-1 protease inhibitors.
P. Jayatilleke, A.C. Nair, R. Zauhar, W.J. Welsh

Application of TLSER molecular descriptors to rate constants.
G.R. Famini, L.Y. Wilson, D. Tran

Computational studies of Raloxifene (Evista®;) derivatives as estrogen receptor modulators: Construction of 3-D-QSAR/CoMFA and hologram QSAR (HQSAR) models as guides for drug design efforts.
W.J. Welsh, S-J. Yu, D.C. Derington, R.J. Greco

Computational study of somatostatin analogs: 3-D QSAR prediction of somatostatin receptor subtype 2 (sst2) binding affinities.
A.C. Nair, S-J. Yu, W.J. Welsh, S. Achilefu

Molecular skeleton analysis and its application for NMDA/glycine/kynurenic-binding complex.
G. Liang, S. Li, Y. Gu, A. Lewin, J.P. Bowen

Prediction of vapor pressure of hydrocarbons and halocarbons from molecular structure.
E.S. Goll, P.C. Jurs

Prediction of hydroxyl radical rate constantsfrom molecular structure.
G.A. Bakken, P.C. Jurs

Monte Carlo studies of stochastic resonance in bimolecular rapid reactions.
H.L. Martinez

Energetics of amino acidation.
E.C.M. Chen, A.K. Evanson, J. Miller

Computational study of ionization potential and proton transfer in small clusters of 2,5-dihydroxybenzoic acid.
E.F. Archibong, G.R. Kinsel, D.S. Marynick

Coenzyme B12 chemistry: Insights from a computational study.
M. Torrent, D.G. Musaev, S-C. Ke, K. Warncke, K. Morokuma

Solvent effects on free energies of solvation for organic solutes using Monte Carlo statistical mechanics simulations and ab initio method.
H-S. Kim

Application of linear-scaling semiempirical, methods to the study of enzyme reaction mechanisms.
S.J. Titmuss, J.E. Gready, A.P. Rendell, A.A. Bliznyuk

Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) model.
P.L. Cummins, J.E. Gready

Combined QM/MM simulations in water and in the active site of a chorismate mutase enzyme: Study of the enzymatic rearrangement and analysis of the factors contributing to catalysis.
C. Alhambra, K. Byun, J. Gao

QM/MM boundaries across covalent bonds: Proton affinities of amino acids and small peptides.
J.H. Jensen, V. Kairys

Simulation of phosphate ester hydrolysis.
P.D. Lyne, O.A. Walsh

Reaction energetics of catechol O-methyltransferase: A combined ab initio/free energy approach.
B. Kuhn, P.A. Kollman

Using the effective fragment-potential model to study the solvation of acetic and formic acids.
M.A. Freitag, M.S. Gordon

Semiexplicit solvation of biomolecules through a surface of active polarons (SOAP).
S.R. Kimura, R.C. Brower, S. Vajda

Efficient algorithm for the calculation of the two-center overlap integrals with noninteger n Slater-type orbitals (NISTOs).
A. Baba-Ahmed, S.M. Mekelleche

Density functional theory studies of hexamine triperoxide diamine.
A. Wierzbicki, E. Cioffi

Modeling the a-chlorothioethers: Potential applications in the synthesis of novel a-amino acids.
D.A. Osborne, A.B. Dribben, D.H. Magers

On the mechanism of Diels-Alder reactions.
A. Baba-Ahmed, F. Berrahoui

Ring strain in the oxadiazetidines.
C.W. Benton, D.H. Magers

Structure of 2-aminonicotinic acid.
W.R. Dreher Jr., E.J. Valente, D.H. Magers

Theoretical studies of the additions of germylenes to ethylene.
M-D. Su, S-Y. Chu

Topology of the charge distribution of the silanol-thiophene Van der Waals complex: Ab initio and DFT study.
H. Soscun, J. Hernandez, O. Castellano

Use of the CURES-EC method in calculating electron affinities of triatomic molecules.
E.C.M. Chen, D.J. Hays, H. Allen

Modeling reactions at solid-liquid interfaces using hybrid QM/MM methods: A comparative study.
R.A. Bryce, K. Wright, I.H. Hillier

C-H bond dissociation enthalpies of substituted phenyl-X and vinyl-X systems.
P.S. Broughton, C.M. Hadad

Chirality in chloro{2-[1-(S)-(dimethylamino)ethyl]phenyl-C1,N} Hg(II).
R. Jiménez-Cataco, E. Aceves-De-Alba

Radical addition and H-atom abstraction processes with polycyclic aromatic hydrocarbons.
P.S. Broughton, C. Barckholtz, C.M. Hadad

Searches on the potential energy surfaces of BNH2, BPH2, AlNH2, and AlPH2.
J.H. Youngblood, C.W. Benton, D.H. Magers

Ab initio study of the adsorption of MNA on H-terminated Si(100) surface modeled by SimHn clusters.
S.M. Black, C. Sapp-Mobley

Basis set and electron correlation effects in electric polarizability and hyperpolarizability calculations for O3, SO2, SeO2, and TeO2.
G. Maroulis, D. Xenides

Electronic structure studies of group 3-5 clusters.
P.P. Korambath, S.P. Karna

Hyperpolarizability of C2X4 (X=H, F, Cl, Br, and I).
G. Maroulis, P. Karamanis

Nonlinear optical properties and molecular vibration of p-conjugated frames: Polyenes and polyynes.
K.S. Kim, J.Y. Lee, S.B. Suh

Photoswitch and nonlinear optical switch: Theoretical studies on diarylethylene derivatives.
K.S. Kim, H.M. Lee, D. Majumdar, J. Kim

Quantum chemical studies of C36 and its hydrogenation products.
M.E. Colvin, N.L. Tran, J.C. Grossman, C.L. Janssen

Are fullerenes and carbon nanotubes viable candidates for h6 metal ligands?
S.K. Goh, D.S. Marynick

Conformational energy surface of 1,3,5-trisilacylohexane and silacyclohexane.
I. Arnason, G.K. Thorarinsson, E. Matern

Simulation of nylon-6 polymerization in homogeneous continuous stirred tank reactors.
J. Lin, T. Chen

Comparative study of dipole moments.
P.M. Todebush, B. Ma, J-H. Lii, J.P. Bowen, N.L. Allinger

Expert system assisted pharmacophore identification.
A.K.T. Ting, P. Johnson, S. Green, R. McGuire, J. Kaur

Wednesday Morning

Bridging the Gap: Theoretical Chemistry to Drug Design

Ph.D. program specifically designed for industrial CADD.
R.S. Pearlman

Computer-aided drug design education and training at the University of Mississippi.
R.D. Sindelar, M.A. Avery, J.K. Buolamwini

Making theoretical chemistry "useful" through computational chemistry.
W.J. Welsh

Road from the graduate school to the industry is paved ...?
A. Tropsha

Nonlinear Optical and Electronic Materials

Linear and nonlinear electrodynamics of noble-metal nanoparticles.
G.C. Schatz, T. Jensen, L. Kelly, A. Lazarides

Generalized tight-binding molecular dynamics simulations of CxByNz nanotube-based electronics and electromechanics.
D. Srivastava

Ab initio calculation of dimensional changes as a function of charge injection for carbon nanotube artificial muscles.
M. Kertesz, G. Sun, J. Kurti, R. Baughman

Electrical properties of distorted carbon nanotubes.
A. Rochefort, P. Avouris, D.R. Salahub

Modeling the influence of intermolecular electrostatic interactions on electric poling induced electro-optic activity.
L.R. Dalton, B.H. Robinson

Ab initio model for solvent effects in organic molecules.
G.P. Das

Two valence bond state models for molecular nonlinear optical properties: Nonequilibrium solvation formulation.
W.H. Thompson, M. Blanchard-Desce, J.T. Hynes

QM/MM Methods

Hybrid quantum mechanical/molecular mechanical scheme based on linear-scaling electronic structure methods.
D.M. York

Nonadiabatic molecular dynamics of charge transfer reactions.
S. Hammes-Schiffer

QM/MM methods for solvation and surface chemistry.
M.S. Gordon, C.H. Choi

Fully quantum mechanical calculations on solvated biomolecular systems: New insights and implications for QM/MM simulation techniques.
A. vanderVaart, K.M. Merz Jr.

QM/MM boundaries across covalent bonds: A frozen LMO-based approach for the effective fragment potential method.
J.H. Jensen, V. Kairys

Theory of a charge-transparent interface between QM and MM regions in combined QM/MM methods of molecular modeling.
I.B. Bersuker

Wednesday Afternoon

Bridging the Gap: Theoretical Chemistry to Drug Design

Computational chemistry in the undergraduate/graduate classroom
T. Holme

Drug docking and other computational methods in an undergraduate/graduate biochemistry course.
P.H. Draves

Needed: Computational chemist, prefer experience in ....
J.B. Dunbar

Finding the needle in a haystack: Synergy between rational and combinatorial drug design.
O.F. Guner, R.D. Brown, E.A. Jamois, M. Waldman

Computational chemistry in a high-throughput drug discovery environment.
E. Hodgkin

Applications of computational chemistry in biotechnology and medical diagnostics.
J.B. Pitner

Nonlinear Optical and Electronic Materials

Hyper-Rayleigh scattering at 1907 nm to measure the first hyperpolarizability of nonlinear optical chromophores.
J.N. Woodford, C.H. Wang

Theoretical investigation of electronic structures and optical band gaps for 1,2-phenylamino squaraine polymers.
X. Duan, D.S. Dudis

Rotational and collision-induced contributions to the third-order nonlinear optical response of liquid CS2.
K. Kiyohara, K. Kamada, K. Ohta

Polymeric Langmuir-Blodgett films for nonlinear optics.
A.M. Ritcey

Electronic structure calculations of materials for optical limiting applications.
K.A. Nguyen, P.N. Day, R. Pachter

Modeling nonlinear optical properties of inorganic complexes.
T. Zhou, T.R. Cundari, H.A. Kurtz

Electrical and optical properties of paramagnetic systems: A time-dependent unrestricted Hartree-Fock study.
S.P. Karna

QM/MM Methods

Simulations of enzymatic reactions and computation of kinetic isotope effects.
J. Gao

Density functional theory applied to very large systems: A QM/MM study of chemical reactivity of zeolites.
N. Ferré, J. Ángyán, X. Assfeld, J-L. Rivail

Modeling of surface reaction with combined-force molecular dynamics.
M. Frenklach

DFT, force fields, and MD for hydrogen bonds, proton transfer, and solvated ions.
D.R. Salahub

Cycloaddition reactions of 1,3-cyclohexadiene on silicon (001) surface using the SIMOMM: Diels-Alder or not?
C.H. Choi, M.S. Gordon

Multiparticle and multidimensional hydrogen wavefunctions.
S.P. Webb, S. Hammes-Schiffer

Thursday Morning

Drug Design and Biomolecules

Molecular docking: A pharmacophoric approach.
B.E. Thomas IV, D. Joseph-McCarthy, M. Belmarsh, D. Moustaka, J.C. Alvarez

Dynamic models of the N-benzyladriamycin-14-valerate complex with the C1b domain of protein kinase C-d.
A.L. Parrill, J.B. Roaten, T. Sweatman, M. Israel

Structure-activity relationships (SAR) for human cyclin-dependent kinase 4 (CDK4)/cyclin D with novel CDK inhibitors using
a CDK4 homology model.
L. Schaffer, P.W. Rose, W.K.M. Chong, L. Li, R.K. Duvadie, J. Nonomiya, D.R. Knighton, R. Ferre, Y.M. Yang, S.S. Chu, K.D. Tucker, W. Sisson, R.M. Aust, C.T. Lewis

Comparative molecular field analysis (CoMFA) QSAR study of conformationally restricted cinnamyl HIV integrase inhibitors.
J.K. Buolamwini

Computational studies on HIV-1 protease inhibitors: Influence of calculated inhibitor-enzyme binding affinities on the statistical quality of 3-D-QSAR comparative molecular field analysis (CoMFA) models.
P. Jayatilleke, A.C. Nair, R. Zauhar, W.J. Welsh

Effect of charge state of His110 and NADPH at the active site of aldose reductase on the binding affinity of tight-binding inhibitor tolrestat.
Y.S. Lee, K. Sugiyama, P.F. Kador

Homology model of Mycobacterium tuberculosis glutamine fructose-6-phosphate amidotransferase (GFAT).
N.G.J. Richards, T.C. Sintjago

Computational strategy for the rational design of HIV-1 protease inhibitors that are effective against mutant enzymes.
A.C. Nair, P. Jayatilleke, R. Zauhar, W.J. Welsh

Molecular modeling and automated receptor docking of selective m-agonists on the m-opioid receptor.
D. Ferguson, G. Subramanian, M. Paterlini

Protein-Protein Interactions

Computer modeling of flexible protein-protein and protein-DNA docking.
M.J.E. Sternberg, P. Aloy, H.A. Gabb, R.M. Jackson, G. Moont, E. Querol, F.X. Aviles

Systematic study of low-resolution recognition in protein-protein complexes.
I.A. Vakser, O.G. Matar, C.F. Lam

Rigid and flexible docking and structural-matching techniques.
R. Nussinov, R. Norel, B. Sandak, G. Verbitsky, H. Wolfson

Estimating protein-protein interactions by mapping interfaces.
R.R. Gabdoulline, R.C. Wade

Protein folding and the influence of secondary structure on hydrogen bond energies and peptide group planarity.
S.W. Rick, R.E. Cachau

QM/MM Methods

Application of free energy perturbation QM/(MM+MD) methods to the study of proton affinities in enzyme-active sites.
P.L. Cummins, J.E. Gready

Proton and hydride ion transfers in biological systems modeled by QM/MM methods.
I.H. Hillier, N.A. Burton, R.M. Nicoll, D.W. Sheppard

Simulations of chemical reactions in proteins and solutions by ab initio and related approaches.
A. Warshel

Investigation of enzyme reactivity using MM, QM/MM and linear scaling approaches: Human fibroblast collagenase.
G. Monard, K.M. Merz Jr.

Ab initio molecular dynamics study on the active site of HIV-1 protease.
S. Piana, P. Carloni

Studying enzyme reactions with a pseudo-bond ab initio QM/MM approach.
Y. Zhang, W. Yang

Thursday Afternoon

General

Impact of computing on organic chemistry and synthesis.
W.T. Wipke

Stereochemistry of nonactin: A computational analysis.
J.M. Goodman, R. Hoyer, A. Burzlaff, R. Omar

Estimation of chemical reduction potentials.
S.H. Hilal, S.W. Karickhoff, L.A. Carreira

Mesoscopic simulation of glass transition for miscible polymer blends.
K.R. Sharma

Entropic difference model during glass transition for partially miscible blends with styrenic systems.
K.R. Sharma

Metallosystems

Web-based resource for metalloprotein research: The metalloprotein site database and browser.
J.M. Castagnetto, S.W. Hennessy, M. Pique, E.D. Getzoff, J.A. Tainer

Computational studies of the electronic structure of the Fe(III) center in nitrile hydratase.
N.G.J. Richards, A.J. Boone

Use of nonstandard parameters for Becke's three-parameter hybrid functional: Its application to density functional studies of transition metals.
E.J. ThomasIII, P. Lane, J.S. Murray, P. Politzer, C.J. O'Connor

PM3(tm) parameterization using genetic algorithms.
J. Deng, T. Cundari, W. Fu Jr.

Computational studies of titanium imidos carbon-hydrogen bond activation.
T.R. Klinckman Jr., T.R. Cundari

Computational investigation of a series of tetrathio-rhodium(III) complexes.
A.R. Lawrence, P.L.M. Plummer

Analysis of strain in main-group cages.
C.W. Earley

Protein-Protein Interactions

Sensitive potential for protein-protein docking.
R. Abagyan, M. Totrov, J. Fernandez-Recio

Predicting macromolecular interactions by a complete, systematic search.
V.A. Roberts, M.E. Pique, J. Mandell, L.F.

Orientational electrostatic steering in protein-protein association.
R.R. Gabdoulline, R.C. Wade

Thermodynamic and kinetic role of desolvation in protein-protein association.
S. Vajda, C.J. Camacho, C. DeLisi

Designing inhibitors of protein-protein interactions based on protein structure-function data.
D.R. Artis

CD8 protein's surface used as a design template for the engineering of bioactive analogs.
B.A. Jameson, A.P. Tretiakova

Protein-protein interactions in the TNF system.
K. Ramnarayan




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