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Completed List of Publications 2003 2002 2001 2000 1999 1998 1997 1996 1995 1994 In Press | Submitted for Publications | In Preparation | Accepted for Publication |
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2003
"The Analysis if Urine Proteomic and Metabonomic Patterns for the Diagnosis of Cystitis," D.A. Lucas, B. Luke, J. Collins, Q.N. Van, J. Klose, G. N. Chmurny, D. A. Prieto, T. P. Conrads, S. K. Burt, S. K. Keay, and T. D. Veenstra, Abstracts of the 51st Conference on Mass Spectrometry and Applied Topics, Montreal, June 2003, pg. 1313.
An Exhaustive DNA Micro-satellite Map of the Human Genome Using High Performance Computing. Jack R. Collins, Robert M. Stephens, Bert Gold, Bill Long, Michael Dean and Stanley K. Burt. Genomics, Vol. 82 Issue 1, July 2003, pg. 10-19.
"Flexible Effective Fragment QM/MM Method: Validation Through the Challenging Tests." A. V. Nemukhin, B. L. Grigorenko, I. A. Topol, S. K. Burt, Journal of Computational Chemistry, 24, No.12, 1410-1420, 2003.
"The Formation of Alkali Metal/Alkaline Earth Cation Water Clusters, M(H2O)1-6, M = Li+, Na+, K+, Mg2+, and Ca2+ : An Effective Fragment Potential (EFP) Case Study. Grant N. Merrill, Simon P. Webb, and Donald B. Bivin, Journal of Physical Chemistry A , 2003, vol. 107, pg. 386-396.
"Fuzzy Structure-Activity Relationships, B.T. Luke, SAR QSAR Environ. Res., 14, 41-57 (2003)
“Identification of Critical Residues of an Immunodominant Region of Echinococcus Granulosus Antigen B.” González-Sapienza Gualberto and Raul E. Cachau, Journal of Biological Chemistry, 278, 20179-20184 (2003).
"Peptide Models. XXXIII. Extrapolation of Low-Level Hartree-Fock Data of peptide Conformation to Large Basis Set SCF, MP2, DFT, and CCSD(T) Results. The Ramachandran Surface of Alanine Dipeptide Computed at Various Levels of Theory." A. Perczel, O. Farkas, I. Jakli, I. A. Topol, I. G. Csizmadia, Journal of Computational Chemistry, ., 24, No.9, 1026-1042, 2003.
"Quantum Chemical Simulations of the Proton Transfer in Water Wires Attached to Molecular Walls." A. V. Nemukhin, B. L. Grigorenko, I. A. Topol, S. K. Burt, Journal of Physical Chemistry B, 107, 2958-2965, 2003.
"TMAP (Tissue Molecular Anatomy Project), an Expression Database for Comparitive Cancer Proteomics," D. Medjahed, B. T. Luke, T. S. Tontesh, G. W. Smythers, D.J. Monroe, and P.F. Lemkin, Proteomics, 3 (2003), 1445-1453.
“Complete Basis Set and Density Functional Determination of the Enthalpy of Formation of the Controversial HO3 Radical: a Discrepancy Between Theory and Experiment” Pablo A. Denis, Martina Kieninger, Oscar N. Ventura, Raul E. Cachau and Geerd H.F. Diercksen, Chemical Physics Letters, 365, 440–449 (2002).
“Density Functional Computational Thermochemistry: Solving the Discrepancy Between MO and DFT Calculations on the Enthalpy of Formation of Sulfine, CH2=S=O.” Oscar N. Ventura, Martina Kieninger, P. A. Denis and Raúl E. Cachau, Chemical Physics Letters, 355(3-4), 207-213 (2002).
"DFT Calculations on Redox Potentials of Disulfide Compounds Directed Against Retroviral Zinc Finger, Recent Advances in Density Functional Methods, Part III, V," I. A. Topol, C. McGrath, E. N. Chertova, S. K. Burt. V. Barone, A. Bencini, P. Fantucci, Eds., World Scientific Publishing Co., pp. 325-338, 2002.
"Energy Profiles for the Rate Limiting Stage of the Serine Protease Prototype Reaction," A. V. Nemukhin, I. A. Topol, S. K. Burt, Int. Journal of Quantum Chemistry, 88, 34-40, 2002.
"Human Topoisomerase I Inhibition: Docking Camptothecin and Derivatives into a Structure-Based Active Site Model," G.S. Laco, J. R. Collins, B.T. Luke, H. Kroth, J. M. Sayer, D. M. Jerina, and Y. Pommier, Biochem. 41, 1428-1435 (2002).
“Ink-Jet Printer Heads for Ultra-Small-Drop Protein Crystallography” E.I. Howard and R. E. Cachau, BioTechniques, 33(5), 1302-1306 (2002).
"Modeling of Biomolecular Systems with the QM/MM Method Based on the Effective Fragment Potential Technique: Proposal of Flexible Fragments," B. L. Grigorenko, A. V. Nemukhin, I. A. Topol, S. K. Burt. Journal of Physical Chemistry A, 106, 10663-10672, 2002.
"Multiconfigurational Nuclear-Electronic Orbital Approach: Incorporation of Nuclear Quantum Effects in Electronic Structure Calculations." Simon P. Webb, Tzvetelin Iordinov, and Sharon Hammes-Schiffer, Journal of Chemical Physics, 2002, vol. 117, pg. 4106-4118.
"On the Origin of Potential Barrier for the Reaction OH- + CO2 -> HCO3- in water: Studies by using Continuum and Cluster Solvation methods," B. T. Luke, in Nature-Inspired Methods in Chemometrics: Genetic Algorithms and Neural Networks, A. V. Nemukhin, I. A. Topol, B. L. Grigorenko, S. K. Burt, Journal of Physical Chemistry B, 106, No. 7, 1734-1740, 2002.
"The Palm Subdomain-based Active Site is Internally Permuted in Viral RNS-dependent RNA Polymerase of an Ancient Lineage," A.E. Gorbalenya, F. M. Pringle, J. L. Zeddam, B. T. Luke, C. E. Cameron, J. Kalmakoff, T. N. Hanzlik, K. H. J. Gordon, and V. K. Ward, Journal of Molecular Biology, 24, 47-62 (2002)
"A QM/MM Approach with Effective Fragment Potentials Applied to the Dipeptide-Water Structures," A. V. Nemukhin, B. L. Grigorenko, A. V. Bochenkova, I. A.Topol, S. K. Burt. Journal of Molecular Structure, THEOCHEM, 581, 167-175, 2002.
"Quantum Chemical Modeling of Reactivity and Selectivity of 1,2-dithiolanes Towards Retroviral and Cellular Zinc Fingers." I. A. Topol, A. V. Nemukhin, S. K. Burt, Molecular Physics, 100, No. 6, 791-797, 2002.
“Regulatory Site of the Lys213 pKa of Saccharomyces Cerevisiae Phosphoenolpyruvate Carboxykinase: Theoretical and Experimental Study.” Fernando D. González-Nilo, Hans Krautwurst, Alejandro Yévenes, Emilio Cardemil, and Raul Cachau, BBA - Proteins and Proteomics, 1599(1-2), 65-71 (2002).
"TMAP (Tissue Molecular Anatomy Project)," D. Medjahed, T.S. Tontesh, G.W. Smythers, B. T. Luke, P. F. Lemkin, and D. J. Monroe, in 2002 Congress of Applied Proteomics, P.M. Palagi et al. (Eds.), 3-5 December 2002, Lausanne, Switzerland (FontisMedia SA, Switzerland) pp. 71-72.
"alpha and 310- Helix Interconversion: A Quantum-Chemical Study on Polyalanine Systems in the Gas Phase and in Aqueous Solvent." I. A. Topol, S. K. Burt, E. Deretey, T.H. Tang, A. Perczel, A. Rashin, I. G. Csizmadia, Journal of American Chemical Society, 123, No. 25, 6054-6060, 2001.
"Charge Distributions in Water and Ion-Water Clusters," A. A. Rashin, I. A. Topol, G. J. Tawa, S. K. Burt, Chemical Physics Letters, 335, 327-333, 2001.
“Density Functional Computational Thermochemistry: Isomerization of Sulfine and Its Enthalpy of Formation.”, Ventura ON, Kieninger M, P.A. Denis and R.E. Cachau, J.Phys.Chem. A 105(43), 9912-9916 (2001).
"Experimental Determination and Calculations of Redox potential Descriptors of Compounds Directed Against Retroviral Zinc Fingers: Implications for Rational Drug Design," I. A. Topol, C. McGrath, E. Chertova, C. Dasenbrock, M. R. LaCourse, M. A. Eissenstat, S. K. Burt, L.E. Henderson, J. R. Casas-Fine, Protein Science, 10, 1434-1445, 2001.
"Hydride Transfer in Liver Alcohol Dehydrogenase: Quantum Dynamics, Kinetic Isotope Effects, and the Role of Enzyme Motion." Salomon R. Billeter, Simon P. Webb, Pratul K. Agarwal, Tzvetelin Iordinov, and Sharon Hammes-Schiffer, Journal of the American Chemical Society, 2001, vol. 123, pg. 11262-11272.
"Hybrid Approach for Including Electronic and Nuclear Quantum Effects in Molecular Dynamics Simulations of Hydrogen Transfer Reactions in Enzymes." Salomon R. Billeter, Simon P. Webb, Tzvetelin Iordinov, Pratul K. Agarwal, and Sharon Hammes-Schiffer,Journal of Chemical Physics,2001, vol. 14, pgs. 6925-6936.
"Interactions of Azodicarbonamide (ADA) Species with the Model Zinc Finger Site: Theoretical Support of the Zinc Finger Domain Destruction in the HIV-1 Nucleocapsid Protein (NCp7) by ADA", I. A. Topol, A. V. Nemukhin, Y. I. Dobrogorskaya, S. K. Burt, Journal of Physical Chemistry B, No. 45, 11341-11350, 2001.
“Linear Scaling DFT Calculations with Numerical Atomic Orbitals.”, P. Ordejón, E. Artacho, R.E. Cachau, J. Gale, A. García, J. Junquera, J. Kohanoff, M. Machado, D. Sanchez-Portal, J. M. Soler and R. Weht, Mat. Res. Soc. Symp. Proc. 677, AA9.6.1-11 (2001).
"Partial Multidimensional Grid Generation Method for Efficient Calculation of Nuclear Wavefunctions." Tzvetelin Iordinov, Salomon R. Billeter, Simon P. Webb, and Sharon Hammes-Schiffer, Chemical Physics Letters, 2001, vol. 338, pg. 389-397.
"Quantum Chemical Investigation of Enzymatic Activity in DNA Polymerase B. A Mechanistic Study." Y.G. Abashkin, J. W. Erickson, S. K. Burt. Journal of Physcial Chemistry B. 2001, 40, 4040-4048.
"The (salen) Mn(III)-catalyzed Epoxidation Reaction as a Multi-channel Process with Different Spin States. Electronic Tuning of Asymmetric Catalysis: a Theoretical Study." Y. G. Abashkin, J. R. Collins, S. K. Burt. J. Inor. Chem. 2001, 40, 4040-4048.
"Titanium Chemistry." Mark S. Gordon, Simon P. Webb, Takako Kudo, Brett M. Bode, Jerzy Moc, Dmitri G. Fedorov, and Gyusung Chung, Computational Organometallic Chemistry, T.R. Cundari, Ed., Marcel-Dekker, Inc. NY, 2001.
"Acidity of Organic Molecules in the Gas Phase and in Aqueous Solvent, .” I. A. Topol, G. J. Tawa, R. A. Caldwell, M. A. Eissenstat, S. K. Burt, Journal of Physical Chemistry A, 104, No. 42, 9619-9624, 2000.
"Calculation of Substitute Effects on pKa Values of Pyrone and Dihydropyrone Inhibitors of HIV-1 Protease.” I. A. Topol, S. K. Burt, A. A. Rashin, J. W. Erickson, Journal of Physical Chemistry A. 104, No. 4, 866-872, 2000.
"Combining Electronic Structure Methods with Calculation of Hydrogen Vibrational Wavefunctions: Application to Hydride Transfer Catalyzed by Liver Alcohol Dehydrogenase." Simon P. Webb, Pratul K. Agarwal, and Sharon Hammes-Schiffer, Journal of Physical Chemistry B, 2000, vol. 104, pg. 8884-8894.
"Computational Studies of the Mechanism for Proton and Hydride Transfer in Liver Alcohol Dehydrogenase." Pratul K. Agarwal, Simon P. Webb, and Sharon Hammes-Schiffer, Journal of the American Chemical Society, 2000, vol. 122, pg. 4803-4812.
"Concertedness and Solvent Effects in Multiple Proton Transfer Reactions: the Formic Acid Dimmer in Solution." J. Kohanoff, S. Koval, D. A. Estrin, D. Laria, Y. G. Abashkin. J. Chem. Phys. 2000, 112(21), 9498-9508.
“Density Functional Computational Thermochemistry. Determination of the Enthalpy of Formation of Sulfine, CH2=S=O, at Room Temperature.” O. N. Ventura, M. Kieninger, R. E. Cachau, and S. Suhai, Chem. Phys. Lett. 329(1-2), 145-153 (2000).
"Fourier-Grid Hamiltonian Multiconfigurational Self-Consistent Field: A Method to Calculate Multidimensional Hydrogen Vibrational Wavefunctions." Simon P. Webb and Sharon Hammes-Schiffer, Journal of Chemical Physics, 2000, vol. 113, pg. 5214-5227.
"Hydrogen Bonding at the Diatomics-in-Molecule Level: Water Clusters," .” B. L. Grigorenko, A. V. Nemukhin, I. A. Topol, S. K. Burt, Journal of Chemical Physics, 113, No.7, 2638-2647, 2000.
"Model of the Catalytic Mechanism of Human Aldose Reductase Based on Quantum Chemical Calculations." R.E.Cachau, E. Howard, P. Barth, A. Mitschler, B. Chevrier, V. Lamour, A. Joachimiak, R. Sanishvili, M. Van Zandt, E. Sibley, D. Moras and A. Podjarny, Journal de Physique IV France, 10, 3-13 (2000).
"The Nonplanarity of the Peptide Group: Molecular Dynamics Simulations with a Polarizable Two-state Model for the Peptide Bond." S.W. Rick and R.E. Cachau, Journal of Chemical Physics. 112(11), 5230-5241 (2000).
"Quantum Chemical Studies of Reactions of the Cyclic Disulfides with the Zinc Finger Domains in the HIV-1 Nucleocapsid Protein (NCp7)," ).” I. A. Topol, A. V. Nemukhin, M. Chao, L. K. Iyer, G. J. Tawa, S. K. Burt, Journal of American Chemical Society, 122, No. 29, 7087-7094, 2000.
"Structural Complexity of H-bonded networks." G.A. Arteca, R.E. Cachau and K. Veluri, Chem.Phys.Lett. 319(5-6), 719-724 (2000).
"Computational Studies of the Domain Movement and the Catalytic Mechanism of Thymidine Phosphorylase." S. W. Rick, Y. G. Abashkin, R. Hildebrandt, S. K. Burt. Proteins: Structure, Function, and Genetis 1999,37, 242-252.
"Intermolecular Self-Interactions of the Titanium Tetrahalides (TiX4, X=F,Cl,Br)." Simon P. Webb and Mark S. Gordon, Journal of the American Chemical Society, 1999, vol. 121, pg. 2552-2560.
"On the Structure and Thermodynamics of Solvated Monoatomic Ions Using a Hybrid Solvation Model." I.A. Topol, G. J. Tawa, S. K. Burt, A. A. Rashin. Journal of Chemical Physics. 111, No. 24, 10998-11014, 1999.
"Solvation of the Menshutkin Reaction: A Rigorous Test of the Effective Fragment Method." Simon P. Webb and Mark S. Gordon, Journal of Physical Chemistry A, 1999, vol. 103, pg. 1265-1273.
"Calculation of the Aqueous Solvation Free Energy of the Proton." G. J. Tawa, I. A. Topol, S. K. Burt, R. A. Caldwell, A. A. Rashin. Journal of Chemical Physics. 109, 4852-4863, 1998.
"Calculation of Relative Binding Free Energies of Peptidic Inhibitors to HIV-1 Protease and its I84V Mutant." G. J. Tawa, I. A. Topol, S. K. Burt, J. W. Erickson. Journal of American Chemistry Society. 120, No.34, 8856-8863, 1998.
"Dynamic Flexibility of Protein-Inhibitor Complexes. A Study of the HIV-1 Protease/KNI-272 Complex.” J. R. Collins, X. Luo, R. Kato. Journal of American Chemistry Society. 120: 12410-12418, 1998.
"The Effect of Spin-Orbit Coupling on the Magnetic Properties of Ti2H6." Simon P. Webb and Mark S.Gordon, Journal of Chemical Physics, 1998, vol. 109, pg. 919-927.
"Molecular Electronic Structure and Energetics of the Isomers of Ti2H6." Simon P. Webb and Mark S. Gordon, Journal of the American Chemical Society, 1998, vol. 120, pg. 3846-3857.
"Proline Cis-Trans Isomerization in Cyclophilin: a One Step Catalytic Mechanism Revealed by a Combined Free Energy Perturbation and Density Functional Study." R. E. Cachau, Y. G. Abashkin. The molecular modeling e-conference 1997-1998, vol.2. (ISSN 0797-9274).
"A Quantum-Mechanical Study of Metal Binding Sites in Zinc Finger Structures." I. A. Topol, J. R. Casas-Finet, R. Gussio, S. K. Burt, J. W. Erickson. Journal of Molecular Structure, Theochem. 423, No. 1-2, 13-28, 1998.
"Building Molecular Charge Distributions from Fragments: Application to HIV-1 Protease Inhibitors." L. Young, I. A. Topol, S. K. Burt, A. A. Rashin. Journal of Computational Chemistry. 18, No. 4, 522-532, 1997.
"Calculation of Absolute and Relative Acidities of Substituted Imidazoles in Aqueous Solvent." I. A. Topol, G. J. Tawa, S. K. Burt, A. A. Rashin. Journal of Physical Chemistry A. 101, No.51, 10075-10081, 1997.
"Density functional study of the mechanisms and the potential energy surfaces of MCH2+ + H2 reactions. The case of cobalt and rhodium (M=Co,Rh)." Y. G. Abashkin, S. K. Burt, N. Russo. J. Phys. Chem. A 1997, 101, 8085-8093.
"Design of Sensitive Fluorogenic Substrates for Human Cathespin D.” S. V. Gulnik, L. I. Suvorov, P. Majer, J. R. Collins, B. P. Kane, D. G. Johnson, J.W. Erickson. FEBS Letters, 413: 379-384, 1997.
"Solvation and the Excited States of Formamide." Morris Krauss and Simon P. Webb, Journal of Chemical Physics, 1997, vol. 107, pg. 5771-5775.
"Structure-based Subsite Specificity Mapping of Human Cathepsin D Using Statine-based Inhibitors." P. Majer, J. R. Collins, S. V. Gulnik, and J. W. Erickson. Protein Science. 6:1458-1466, 1997.
"An Effective Fragment Method for Modeling Solvent Effects in Quantum Mechanical Calculations." Paul N. Day, Jan H. Jensen, Mark S. Gordon, Simon P. Webb, Walter J. Stevens, Morris Kraus, David R. Garmer, Harold Basch, and Dora Cohen, Journal of Chemical Physics, 1996, vol. 105, pg. 1968-1986.
"Gaussian Density Functional Method: an Alternative Tool for the Prediction of Physico-chemical Properties." N. Russo, Y.G. Abashkin, P. Calaminici, T. Mineva, E. Sicilia, M. Toscano in Recent Advances in Density Functional Methods (Ed. D.Chong), World Scientific Pub. Comp., Singapore, N.Y. 1996, p.100-121.
"Structure and Bonding of the Remarkable Donor-acceptor Compelxes XBeO (X=NH3, NMe3, CO, N2, C2H2, C2H4, H2, H2CO, O2)." G. Frenking, S. Dapprich, K. F. Kohler, W. Koch, J. R. Collins. Molecular Physics. 89:1245-1263, 1996.
"Structure and Inhibition of Plasmepsin II, a Hemoglobin-degrading Enzyme from Plasmodium Falciparum." A. Silva, A. Y. Lee, S. V. Gulnik, P. Majer, J. R. Collins, T. N. Bhat, P. J. Collins, R. E. Cachau, K. E. Luker, I. Y. Gluzman, S. E. Francis, A. Oksman, D. E. Goldberg, and J. W. Erickson. National Acad. Science. USA 93:10034-9, 1996.
"Activated Dynamics of Flap Opening in HIV-1 Protease." J. R. Collins, S. K. Burt, and J. W. Erickson. Advances in Experimental Medicine and Biology. 362:455-460, 1995.
"Constrained Optimization Procedure for Finding Transition States and Reaction Pathways in the Framework of Gaussian Based Density Functional Method." Y.G. Abashkin, N. Russo, E. Sicilia, M. Toscano in Modern Density Functional Theory: A Tool for Chemistry. Theoretical and Computational Chemistry. Vol. 2. (Ed. J. M. Seminario and P. Politzer), Elsevier, New York, 1995, p.255-272.
"Density Functional Modeling of Ligand-metal Interactions and Enzymatic Activities in Metalloenzymes. Peptide Bond Cleavage by Carboxypeptidase A." Y. G. Abashkin, S. K. Burt, J. R. Collins, R. E. Cachau, N. Russo, J. W. Erickson in Metal-ligand interactions - structure and reactivity (Ed. N. Russo and D. Salahub), Kluwer, 1995, p.1-22.
"The Dimerization of TiH4." Simon P. Webb and Mark S. Gordon, Journal of the American Chemical Society, 1995, vol. 117, pg. 7195-7201.
"Flap Opening in HIV-1 Protease Simulated by 'Activated' Molecular Dynamics." J. R. Collins, S. K. Burt, and J. W. Erickson. National Structural Biology. 2:334-8, 1995.
"Transition States Localization by Density Functional Method. Applications to Isomerization and Symmetry-forbidden Reactions." Y. G. Abashkin, N. Russo, M. Toscano. Theor. Chim. Acta 1995, 19, 179-186.
"Density Functional Treatment of Water-carbon Dioxide Van Der Waals Complex. Y. G. Abashkin, F. Mele, N. Russo, M. Toscano. Inter. J. Quantum Chem. 1994, 52, 1011-1015.
"Thioanisole Sulfoxidation by Cytochrome P450cam (CYP101)." J. A. Fruetel, Y. T. Chang, J. R. Collins, G. H. Loew and P.R. Ortiz de Montellano. Journal of American Chemistry Society. 116:11643-8, 1994.
"Transition State Structures and Reaction Profiles Form Constrained Optimization Procedure. Implementation in the Framework of Density Functional Theory." Y. G. Abashkin, N. Russo. J. Chem. Phys. 1994, 100(6), 4477-4483.
"Transition States and Energy Barriers From Density Functional Studies: Representative Isomerization Reactions." Y. G. Abashkin, N. Russo, M. Toscano. Inter. J. Quantum Chem. 1994, 52, 695-704.
"Anion-Water Clusters A-(H2O)1-6, A = OH, F, SH, Cl, and Br. An Effective Fragment Potential Test Case." Grant. N. Merrill and Simon P. Webb Journal of Physical Chemistry A, in press.
"Applying Genetic Algorithms and Neural Networks to Chemometric Problems," B. T. Luke, in Nature-Inspired Methods in Chemometrics: Genetic Algorithms and Neural Networks, R. Leardi (Ed.), (Elsevier, The Netherlands) Chapter 12, in press.
"A Derivation of the Frozen-orbital Unrestricted Open Shell and Restricted Closed Shell MP2 Analytic Gradient Expressions." Christine M. Aikens, S. P. Webb, Rob L. Bell, Graham D. Fletcher, Michael W. Schmidt, and Mark S. Gordon, Theoretical Chemistry Accounts, in press.
“DYNGA: a General Purpose QM-MM-MD program. I. Application to Water” Claudia L. Parker, Oscar N. Ventura, Stanley K. Burt and Raúl E. Cachau, Molecular Physics, in press (2003).
"Genetic Algorithms and Beyond," in Nature-Inspired Methods in Chemometrics: Genetic Algorithms and Neural Networks", B. T. Luke, R. Leardi (Ed.), (Elsevier, The Netherlands) Chapter 1, in press.
“Structural information content at high resolution: MAD vs. Native” A. Podjarny, T. Schneider, R.E. Cachau and A. Joachimiak, Methods in Enzymology, in press (2003).
"Analysis of Homocamptothecin Inhibition of Human Topoisomerase I via Novel Derivatives and Modeling Studies," G.S. Laco, W. Du, G. Kohlhagen, J. R. Collins, B. T. Luke, H. Kroth, J.M. Sayer, D.M. Jerina, T. G. Burke, D. P. Curran, and Y. Pommier, J. Biol. Chem., submitted for publication.
"Complete Nucleotide Sequence of Euprosterna elaesa Virus Establishes it Is a Member of a New Group of Insect RNA Viruses," J.L. Zeddam, F.M. Pringle, K.H.J. Gordon, V.K. Ward, B.T. Luke, A.E. Gorbalenya, and T.N. Hanzlik, J. Gen. Virol., submitted for publication.
"Design of Full-sized Cyclic Inhibitors of Human Cathepsin D.” P. Majer, J. R. Collins, S. V. Gulnik, A. Y. Lee, and J. W. Erickson. (to be submitted).
“Peptide bond hydrolysis by HIV-1 protease” D. Medjahed, S. Gulnik, R.E. Cachau, A. Lee, J.W. Erickson and A. M. Silva, Biochemistry and Cell Biology), submitted for publication.
"(Salen)Mn-Catalyzed Epoxidation of Alkenes: a Two Zone Process with Different Spin State Channels as Suggested by DFT Study." Y. G. Abashkin, S. K. Burt. Submitted to J. Am. Chem. Soc.
"(Salen)Mn(III) compounds as synthetic catalase mimetics. Tuning for greater therapeutic efficacy: a DFT study." Y. G. Abashkin, S. K. Burt. Will be submitted.
"Serum Proteomic Profiling: Search for Celecoxib-Modulated Targets and Response Predictors." Z. Xiao, B. T. Luke, G. Izmirlian, A. Umar, P. Lynch, R. Phillips, S. Patterson, T. P. Conrads, T. D. Veenstra, P. Greenwald, E. T. Hawk, and I. U. Ali, Nature Medicine, submitted for publication.
"A Survey of Techniques for Extracting Information from Large Proteomic Datasets," B. T. Luke, in Informatics in Proteomics, S. Srivasta (Ed.), (Marcel Dekker, New York), Chapter 19, submitted for publication.
"ClassCK: The Classifier Construction Kit," B. T. Luke, in preparation.
"Detecting Outliers in Spectroscopic Metabolomic and Metabonomic Datasets," B. T. Luke, J. R. Collins, and S. K. Burt, in preparation.
"The Use of Urine Metabonomic Patterns for the Diagnosis of Interstitial and Bacterial Cystitis," D. A. Lucas, B. T. Luke, J. R. Collins, Q. N. Van, G. N. Chmurny, T. P. Conrads, S. K. Burt, S. K. Keay, and T. D. Veenstra, in preparation.
"Direct Configuration Interaction and Multi-Configurational Self-Consistent-Field Method for Multiple Active Spaces with Variable Occupations. I. Method." Joseph Ivanic, Journal of Chemical Physics. Accepted.
"Direct Configuration Interaction and Multi-Configurational Self-Consistent-Field Method for Multiple Active Spaces with Variable Occupations. I. Application to oxoMn(salen) and N2O4." Joseph Ivanic, Journal of Chemical Physics. Accepted.
“First 0.66 Å Resolution Structure of an Enzyme Reveals Aldose Reductase Catalytic Mechanism” E.I. Howard, R. Sanishvili, R.E. Cachau, P. Barth, A. Mitschler, B. Chevrier, V. Lamour, A. Joachimiak, M. Van Zandt, E. Sibley, D. Moras and A. Podjarny, PROTEINS, accepted for publication 2003.
“Structural Bioinformatics: Obtaining 3D Information From Multiple Sequences Using a Feedback Restrained Molecular Dynamics Approach.” R.E. Cachau, G.Gonzalez-Sapienza, S.K. Burt and O.N. Ventura, Cellular and Molecular Biology, accepted for publication (2003).
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