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