ABCC Publication: Completed List of Publications

2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 |

2005

Yuri G. Abashkin, Stanley K. Burt. "(Salen)Mn(III) compound as a nonpeptidyl mimic of catalase. Tuning for greater therapeutic efficacy: a theoretical study.." Inorg. Chem. Volume March (2005)

B.L. Grigorenko, A.V. Nemukhin, Raul E. Cachau, Igor A. Topol, and Stanley K. Burt. "Computational study of a transition state analog of phosphoryl transfer in the Ras-RasGap Complex: AlFx vs MgF3-." J. Molec. Mod.. In Press.

B.L. Grigorenko, A.V. Nemukhin, Igor A. Topol, Raul E. Cachau, and Stanley K. Burt. "QM/MM Modeling the Ras-GAP Catalized Hydrolysis of Guanosine Triphosphate." Proteins: Structure, Function, and Genetics. In Press.

J. Vaidyanathan, T. K. Vaidyanathan, Narayana Subbu and Sarangan Ravichandran . "A computational and experimental analysis of ligand binding to type 1 collagen." Current Computer - Aided Drug Design. Accepted for Publication.

Teresa Duda, V. Venkataraman, Sarangan Ravichandran and R.K. Sharma. "ATP-Regulated Module (ARM) of the Atrial Natriuretic Factor Receptor Guanylate Cyclase." Peptides (Special Edition of Guanylate Cyclase). In Press.

G. Krishnamoorthy, Simon P. Webb, T. Nguyen, P. K. Chowdhury, M. Halder, N. J. Wills, S. Carpenter, G. A. Kraus, M.S. Gordon, and J. W. Petrich. "Synthesis of Hydroxy and Methoxy Perylene Quinones, Their Spectroscopic and Computational Characterization, and Their Antiviral Activity." Photochemistry and Photobiology. Volume 81 (2005): 924-933.

Simon P. Webb. "Ab Initio Electronic Structure Theory as an Aid to Understanding Excited State Hydrogen Transfer in Moderate to Large Systems." Theoretical Chemistry Accounts. Accepted for Publication.

2004

Yuri G. Abashkin and Stanley K. Burt. ""(Salen)Mn-Catalyzed Epoxidation of Alkenes: a Two Zone Process with Different Spin State Channels as Suggested by DFT Study"." Org. Lett.. Volume 6 (2004): 59-62.

Michael V. Pak, Chet Swalina, Simon P. Webb, and Sharon Hammes-Schiffer. "Application of the Nuclear-Electronic Orbital Method to Hydrogen Transfer Systems: Multiple Centers and Multiconfigurational Wavefunctions." Chemical Physics. Volume 304 (2004): 227.

Grant N. Merrill and Simon P. Webb. "The Application of the Effective Fragment Potential Method to Molecular Anion Solvation: A Study of Ten Oxyanion-Water Clusters, A-(H2O)1-4." Journal of Physical Chemistry A. Volume 108, 5 (2004): 833.

Hui Li, Simon P. Webb, Joseph Ivanic, and Jan H. Jensen. "The Determinants of the Relative Reduction Potentials of Type-1 Copper Sites in Proteins." Journal of American Chemical Society. Volume 126 (2004): 8010.

Djamel Medjahed, Peter F. Lemkin, Gary W. Smythers, and David J. Munroe. "Looking for cancer clues in publicly accessible databases." Comparative and Functional. Volume 5 (2004): 196-200.

Yuri G. Abashkin, Stanley K. Burt. "(Salen)Mn(III) compound as a nonpeptidyl mimic of catalase: DFT study of the metal oxidation by a peroxide molecule." Journal of Physical Chemistry B. Volume 108 (2004): 2708-2711.

Joseph Ivanic, Jack R. Collins, and Stanley K. Burt. "A Theoretical Study of the Low Lying Electronic States of oxoX(salen) (X = Mn, Mn–, Fe and Cr–)." Journal of Physical Chemistry A. Volume 108 (2004)

Joseph E. Saveedra, D. Scott Bohle, Kamilah N. Smith, Clifford George, Jack R. Deschamps, Damion Parrish, Joseph Ivanic, Yan-Ni Wang, Michael L. Citro, Larry K. Keefer. "Chemistry of the Diazeniumdiolates. O- versus N-Alkylation of the RNH[N(O)NO]– Ion." Journal of American Chemical Society. Volume 126 (2004): 12880.

A.V. Nemukhin, B.L. Grigorenko, Igor A. Topol, Stanley K. Burt. "QM/MM modeling of the glutathione – hydroxymethyl radical reaction in water." Phys. Chem. Chem. Phys. Volume 6 (2004): 1031-1038.

A.V. Nemukhin, B.L. Grigorenko, A.V. Rogov, Igor A. Topol, Stanley K. Burt. "Modeling of the serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method." Theoretical Chemistry Accounts. Volume 111, 1 (2004): 36-48.

Igor A. Topol, Raul E. Cachau, A.V. Nemukhin, B.L. Grigorenko, and Stanley K. Burt. "Quantum chemical modeling of the GTP hydrolysis by the RAS-GAP protein complex." BBA - Proteins and Proteomics. Volume 1700 (2004): 125-136.

Akagi, K., T. Suzuki, Robert M. Stephens, N. A. Jenkins and N. G. Copeland. "RTCGD: retroviral tagged cancer gene database." Nucleic Acids Research. Volume 32 (2004): D523-D527.

Nemukhin, A. V., B. L. Grigorenko, A. V. Rogov, Igor A. Topol and Stanley K. Burt. "Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method." Theoretical Chemistry Accounts. Volume 111, 1 (2004): 36-48.

Howard, E. I., R. Sanishvili, Raul E. Cachau, A. Mitschler, B. Chevrier, P. Barth, V. Lamour, M. Van Zandt, E. Sibley, C. Bon, D. Moras, T. R. Schneider, A. Joachimiak and A. Podjarny. "Ultrahigh resolution drug design I: Details of interactions in human aldose reductase-inhibitor complex at 0.66 angstrom." Proteins-Structure Function and Bioinformatics. Volume 55, 4 (2004): 792-804.

Kohanoff, J. and Raul E. Cachau. "Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model." Molecular Physics. (2004)

Podjarny, A., Raul E. Cachau, T. Schneider, M. Van Zandt and A. Joachimiak. "Subatomic and atomic crystallographic studies of aldose reductase: implications for inhibitor binding." Cellular and Molecular Life Sciences. Volume 61, 7-8 (2004): 763-773.

Haiyan Yang, Li-Rong Yu, David A. Lucas, Luanne Lukes, Mindy Lancaster, King C. Chan, Haleem J. Issaq, Ming Yi, Robert M. Stephens, Thomas P. Conrads, Timothy D. Veenstra, and Kent W. Hunter. "Parallel analysis of transcript and translation profiles: Identification of metastasis-related signal pathways differentially regulated by drug and genetic modifications." . Submitted for Publication.

Albino Bacolla, Jack R. Collins, Ming Yi, Robert M. Stephens, John P. Jakupciak, Michael Dean, and Robert D. Wells. "More than 140 genes contain at least 250 base-pairs of uninterrupted purines.pyrimidines in the human genome." . In Preparation.

Kelly A. Conrads, Ming Yi, Kerri A. Simpson†, David A. Lucas, Timothy D. Veenstra, Robert M. Stephens, Thomas P. Conrads and George R. Beck Jr. "A combined proteome and microarray investigation of inorganic phosphate-induced pre- osteoblast cells." . Submitted for Publication.

Ming Yi, Horton, J.D., Cohen J.C, and Hobbs H.H, and Robert M. Stephens. "WholePathwayScope: A comprehensive pathway-based analysis tool for high-throughput data." . Submitted for Publication.

GC Davies, SA Ettenberg, AO Coats, M Mussante, Sarangan Ravichandran, Jack R. Collins, MM Nau, S Lipkowitz. "Cbl-b interacts with ubiquitinated proteins; differential functions of the UBA domains of c-Cbl and Cbl-b." Oncogene. Volume 23, 42 (2004): 7104-7115.

Krzystof Jozawiak, Sarangan Ravichandran, Jack R. Collins and I.W. Wainer. "Interaction of noncompetitive inhibitors with an immobilized alpha3beta4 nicotinic acetylcholine receptor investigated by affinity chromatography, quantitative-structure activity relationship analysis, and molecular docking." Journal of Medicinal Chemistry. Volume 47, 16 (2004): 4008-4021.

2003

Jack R. Collins, Robert M. Stephens, Bert Gold, Bill Long, Michael Dean and Stanley K. Burt. "An Exhaustive DNA Micro-satellite Map of the Human Genome Using High Performance Computing." Genomics. Volume 8, 1 (2003): 10-19.

Grant N. Merrill, Simon P. Webb and Donald B. Bivin. "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." Journal of Physical Chemistry A. Volume 107 (2003): 386-396.

Brian T. Luke. "Fuzzy Structure-Activity Relationships." SAR QSAR Environmental Research. Volume 14 (2003): 41-57.

González-Sapienza Gualberto and Raul E. Cachau. "Identification of Critical Residues of an Immunodominant Region of Echinococcus Granulosus Antigen B." Journal of Biological Chemistry. Volume 278 (2003): 20179-20184.

A. Perczel, O. Farkas, I. Jakli, Igor A. Topol and I. G. Csizmadia. "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." Journal of Computational Chemistry. Volume 24, 9 (2003): 1026-1042.

D. Medjahed, Brian T. Luke, T. S. Tontesh, G. W. Smythers, D. J. Monroe and P.F. Lemkin. "TMAP (Tissue Molecular Anatomy Project), an Expression Database for Comparitive Cancer Proteomics." Proteomics. Volume 3 (2003): 1445-1453.

Grant. N. Merrill and Simon P. Webb. "Anion-Water Clusters A-(H2O)1-6, A = OH, F, SH, Cl, and Br. An Effective Fragment Potential Test Case." Journal of Physical Chemistry A. Volume 107 (2003): 7852-7860.

Brian T. Luke. "Applying Genetic Algorithms and Neural Networks to Chemometric Problems." Nature-Inspired Methods in Chemometrics: Genetic Algorithms and Neural Networks. In Press.

Christine M. Aikens, Simon P. Webb, Rob L. Bell, Graham D. Fletcher, Michael W. Schmidt and Mark S. Gordon. "A Derivation of the Frozen-orbital Unrestricted Open Shell and Restricted Closed Shell MP2 Analytic Gradient Expressions." Theoretical Chemistry Accounts. Volume 110 (2003): 233-253.

Brian T. Luke and R. Leardi. "Genetic Algorithms and Beyond," in Nature-Inspired Methods in Chemometrics: Genetic Algorithms and Neural Networks." In Press.

A. Podjarny, T. Schneider, Raul E. Cachau and A. Joachimiak. "Structural Information Content at High Resolution: MAD vs. Native." Methods in Enzymology. In Press.

G. S. Laco, W. Du, G. Kohlhagen, Jack R. Collins, Brian T. Luke, H. Kroth, J. M. Sayer, D. M. Jerina, T. G. Burke, D. P. Curran and Y. Pommier. "Analysis of Homocamptothecin Inhibition of Human Topoisomerase I via Novel Derivatives and Modeling Studies." Journal of Biological Chemistry. Submitted for Publication.

J. L. Zeddam, F. M. Pringle, K. H. J. Gordon, V. K. Ward, Brian T. Luke, A. E. Gorbalenya and T. N. Hanzlik. "Complete Nucleotide Sequence of Euprosterna elaesa Virus Establishes it Is a Member of a New Group of Insect RNA Viruses." Jounal of Gen. Virol. Submitted for Publication.

P. Majer, Jack R. Collins, S. V. Gulnik, A. Y. Lee and J. W. Erickson. "Design of Full-sized Cyclic Inhibitors of Human Cathepsin D." Submitted for Publication.

D. Medjahed, S. Gulnik, Raul E. Cachau, A. Lee, J.W. Erickson and A. M. Silva. "Peptide Bond Hydrolysis by HIV-1 Protease." Biochemistry and Cell Biology. Submitted for Publication.

Z. Xiao, Brian T. Luke, G. Izmirlian, A. Umar, P. Lynch, R. Phillips, S. Patterson, T. P. Conrads, T. D. Veenstra, P. Greenwald, E. T. Hawkand I. U. Ali. "Serum Proteomic Profiling: Search for Celecoxib-Modulated Targets and Response Predictors." Nature Medicine. Submitted for Publication.

Brian T. Luke. "A Survey of Techniques for Extracting Information from Large Proteomic Datasets." Informatics in Proteomics. Submitted for Publication.

Brian T. Luke. "ClassCK: The Classifier Construction Kit." In Preparation.

Brian T. Luke, Jack R. Collins and Stanley K. Burt. "Detecting Outliers in Spectroscopic Metabolomic and Metabonomic Datasets." In Preparation.

D. A. Lucas, Brian T. Luke, Jack R. Collins, Q. N. Van, G. N. Chmurny, T. P. Conrads, Stanley K. Burt, S. K. Keay and T. D. Veenstra. "The Use of Urine Metabonomic Patterns for the Diagnosis of Interstitial and Bacterial Cystitis." In Preparation.

E. I. Howard, R. Sanishvili, Raul E. Cachau, P. Barth, A. Mitschler, B. Chevrier, V. Lamour, A. Joachimiak, M. Van Zandt, E. Sibley, D. Moras and A. Podjarny. "First 0.66 Å Resolution Structure of an Enzyme Reveals Aldose Reductase Catalytic Mechanism." Proteins: Structure, Function, and Genetics. Accepted for Publication.

Volfovsky N, Haas BJ, and Salzberg SL. "Computational discovery of internal micro-exons." Genome Research. Volume 13, 6a (2003): 1216.

The Rice Chromosome 10 Sequencing Consortium. "In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10." Science. Volume 300 (2003): 1566-1569.

Djamel Medjahed, Gary W. Smythers, Douglas A. Powell, Robert M. Stephens, Peter F. Lemkin, and David J. Munroe. "VIRTUAL2D: A web-accessible predictive database for proteomics analysis." Proteomics. Volume 3 (2003): 129-138.

Djamel Medjahed, Brian T. Luke, T. S. Tontesh, Gary W. Smythers, David J. Munroe, and Peter F. Lemkin. "Tissue Molecular Anatomy Project (TMAP): an expression." Proteomics. Volume 3 (2003): 1445-1453.

Q. N. Van, J. R. Klose, D. A. Lucas, D. A. Prieto, Brian T. Luke, Jack R. Collins, Stanely K. Burt, G. N. Chmurny, H. J. Issaq, T. P. Conrads, T. D. Veenstra and S. K. Keay. "The use of urine proteomic metabonomic patterns for the diagnosis of interstitial cyatitis and bacterial cystitis." Disease Markers. Volume 19 (2003): 169-83.

Joseph Ivanic and Klaus Ruedenberg. "A New MCSCF Method based on Full Optimizations of Successive Jacobi Rotations." Journal of Computational Chemistry. Volume 24 (2003): 1250.

Laimutis Bytautas, Joseph Ivanic, and Klaus Ruedenberg. "Split-Localized Orbitals Yield Stronger Configuration Interaction Convergence than Natural Orbitals." Journal of Chemical Physics. Volume 119 (2003): 8217.

Joseph Ivanic. "CI and MCSCF Method for Multiple Active Spaces with Variable Occupations. I. Theory." Journal of Chemical Physics. Volume 119 (2003): 9364.

Joseph Ivanic. "Direct CI and MCSCF Method for Multiple Active Spaces with Variable Occupations. II. Application to oxoMn(salen) and N2O4." Journal of Chemical Physics. Volume 119 (2003): 9377.

Yanni N. Wang, D. S. Bohle, C. L. Bonifant, G. N. Chmurny, Jack R. Collins, K. M. Davies, J. Deschamps, J. L. Flippen-Anderson, L. K. Keefer, J. R. Klose, J. E. Saavedra, D. Waterhouse, and Joseph Ivanic. "Chemistry of the Diazeniumdiolates. Z  E Isomerism." Journal of American Chemical Society. Accepted for Publication.

Yanni Wang, Igor A. Topol, Jack R. Collins, and Stanley K. Burt. "Theoretical Studies on the Hydrolysis of Mono-phosphate and Tri-phosphate in Gas Phase and Aqueous Solution." Journal of American Chemical Society. Volume 125, 43 (2003): 13265-13273.

A.V. Nemukhin, B.L. Grigorenko, Igor A. Topol, Stanley K. Burt. "Flexible effective fragment QM/MM method: Validation through the challenging tests." Journal of Computational Chemistry. Volume 24, 12 (2003): 12.

Dewey, S. R., P. L. Kennedy and Robert M. Stephens. "Are dawn vocalization surveys effective for monitoring goshawk nest-area occupancy?." Journal of Wildlife Management. Volume 62, 2 (2003): 390-397.

Robert M. Stephens, A. W. Alldredge and G. E. Phillips. "Aggressive interactions of Rocky Mountain Elk, Cervus elaphus nelsoni, during the calving season toward Mule Deer, Odocoileus hemionus, in Central Colorado." Canadian Field-Naturalist. Volume 117, 2 (2003): 316-317.

Yuhki, N., T. Beck, Robert M. Stephens, Y. Nishigaki, K. Newmann and S. J. O'Brien. "Comparative genome organization of human, murine, and feline MHC class II region." Genome Research. Volume 13, 6 (2003): 1169-1179.

Yuri G. Abashkin and Stanley K. Burt. "Mn(salen)-catalyzed epoxidation reaction as a multi-channel process. Electronic tuning of asymmetric catalysis: A theoretical study." Abstracts of Papers of the American Chemical Society. Volume 226 (2003): U753-U753.

Raul E. Cachau, G. Gonzalez-Sapienza, Stanley K. Burt and O. N. Ventura. "A new addition to the structural bioinformatics toolbox: 3D models of short bioactive peptides from multiple sequences using feedback restrained molecular dynamics (FRMD)." Cellular and Molecular Biology. Volume 49, 6 (2003): 973-983.

Grigorenko, B., A. V. Nemukhin, Igor A. Topol and Stanley K. Burt. "Practical implementation of the flexible effective fragment QM/MM method for modeling chemical reactions in condensed phases." Abstracts of Papers of the American Chemical Society. Volume 226 (2003): U306-U306.

Nemukhin, A. V., B. Grigorenko, Igor A. Topol and Stanley K. Burt. "Modeling chemical reactions in proteins by the QM/MM method based on the flexible effective fragment potential technique." Abstracts of Papers of the American Chemical Society. Volume 226 (2003): U271-U272.

Nemukhin, A. V., B. L. Grigorenko, Igor A. Topol and Stanley K. Burt. "Quantum chemical simulations of the proton transfer in water wires attached to molecular walls." Journal of Physical Chemistry B. Volume 107, 13 (2003): 2958-2965.

Parker, C. L., O. N. Ventura, Stanley K. Burt and Raul E. Cachau. "DYNGA: a general purpose QM-MM-MD program. I. Application to water." Molecular Physics. Volume 101, 17 (2003): 2659-2668.

Yanni Wang, Jack R. Collins and Stanley K. Burt. "Theoretical study on the roles of divalent metal-ions in GTP hydrolysis." Abstracts of Papers of the American Chemical Society. Volume 226 (2003): U442-U442.

Raul E. Cachau, G. Gonzalez-Sapienza, Stanley K. Burt and O. N. Ventura. "Structural Bioinformatics: Obtaining 3D information from multiple sequences using a feedback restrained molecular dynamics approach." Cellular and Molecular Biology. Volume 49, 6 (2003): 973-983.

Denis, P. A., M. Kieninger, O. N. Ventura, Raul E. Cachau and G. H. F. Diercksen. "Complete basis set and density functional determination of the enthalpy of formation of the controversial HO3 radical. A discrepancy between theory and experiment (vol 365, pg 440, 2002)." Chemical Physics Letters. Volume 377, 3-4 (2003): 3-4.

Gonzalez-Sapienza, G. and Raul E. Cachau. "Identification of critical residues of an immunodominant region of Echinococcus granulosus antigen B." Journal of Biological Chemistry. Volume 278, 22 (2003): 20179-20184.

Podjarny, A., T. R. Schneider, Raul E. Cachau and A. Joachimiak. "Structural information content at high resolution: MAD versus native." Macromolecular Crystallography, Pt D. Volume 374 (2003): 321-341.

Irving W.Wainer, Krzysztof Jozwiak, Sarangan Ravichandran, Jack R. Collins. "Computer based model for identification and characterization of non-competitive inhibitors of nicotinic acetylcholine receptor." Patent. (2003)

2002

Pablo A. Denis, Martina Kieninger, Oscar N. Ventura, Raul E. Cachau and Geerd H.F. Diercksen. "Complete Basis Set and Density Functional Determination of the Enthalpy of Formation of the Controversial HO3 Radical: a Discrepancy Between Theory and Experiment." Chemical Physics Letters. Volume 365 (2002): 440–449.

Oscar N. Ventura, Martina Kieninger, P. A. Denis and Raúl E. Cachau. "Density Functional Computational Thermochemistry: Solving the Discrepancy Between MO and DFT Calculations on the Enthalpy of Formation of Sulfine, CH2=S=O." Chemical Physics Letters. Volume 355, 3-4 (2002): 207-213.

Igor A. Topol, C. McGrath, E. N. Chertova, Stanley K. Burt, V. Barone, A. Bencini, P. Fantucci and Eds. "DFT Calculations on Redox Potentials of Disulfide Compounds Directed Against Retroviral Zinc Finger, Recent Advances in Density Functional Methods, Part III, V." World Scientific Publishing Company. (2002): 325-338.

A. V. Nemukhin, Igor A. Topol and Stanley K. Burt. "Energy Profiles for the Rate Limiting Stage of the Serine Protease Prototype Reaction." International Journal of Quantum Chemistry. Volume 88 (2002): 34-40.

G.S. Laco, Jack R. Collins, Brian T. Luke, H. Kroth, J. M. Sayer, D. M. Jerina and Y. Pommier. "Human Topoisomerase I Inhibition: Docking Camptothecin and Derivatives into a Structure-Based Active Site Model." Biochemistry. Volume 41 (2002): 1428-1435.

E.I. Howard and Raul E. Cachau. "Ink-Jet Printer Heads for Ultra-Small-Drop Protein Crystallography." BioTechniques. Volume 33, 5 (2002): 1302-1306.

B. L. Grigorenko, A. V. Nemukhin, Igor A. Topol and Stanley K. Burt. "Modeling of Biomolecular Systems with the QM/MM Method Based on the Effective Fragment Potential Technique: Proposal of Flexible Fragments." Journal of Physical Chemistry A. Volume 106 (2002): 10663-10672.

Simon P. Webb, Tzvetelin Iordinov and Sharon Hammes-Schiffer. "Multiconfigurational Nuclear-Electronic Orbital Approach: Incorporation of Nuclear Quantum Effects in Electronic Structure Calculations." Journal of Chemical Physics. Volume 117 (2002): 4106-4118.

Brian T. Luke, A. V. Nemukhin, Igor A. Topol, B. L. Grigorenko and Stanley K. Burt. "On the Origin of Potential Barrier for the Reaction OH- + CO2 -> HCO3- in water: Studies by Using Continuum and Cluster Solvation Methods." Journal of Physical Chemistry B. Volume 106, 7 (2002): 1734-1740.

A. E. Gorbalenya, F. M. Pringle, J. L. Zeddam, Brian T. Luke, C. E. Cameron, J. Kalmakoff, T. N. Hanzlik, K. H. J. Gordon and V. K. Ward. "The Palm Subdomain-based Active Site is Internally Permuted in Viral RNS-dependent RNA Polymerase of an Ancient Lineage." Journal of Molecular and Cellular Biology. Volume 24 (2002): 47-62.

A. V. Nemukhin, B. L. Grigorenko, A. V. Bochenkova, Igor A. Topol and Stanley K. Burt. "A QM/MM Approach with Effective Fragment Potentials Applied to the Dipeptide-Water Structures." Journal of Molecular Structure. Volume 581 (2002): 167-175.

Igor A. Topol, A. V. Nemukhin and Stanely K. Burt. "Quantum Chemical Modeling of Reactivity and Selectivity of 1,2-dithiolanes Towards Retroviral and Cellular Zinc Fingers." Molecular Physics. Volume 100, 6 (2002): 791-797.

Fernando D. González-Nilo, Hans Krautwurst, Alejandro Yévenes, Emilio Cardemil and Raul E. Cachau. "Regulatory Site of the Lys213 pKa of Saccharomyces Cerevisiae Phosphoenolpyruvate Carboxykinase: Theoretical and Experimental Study." BBA - Proteins and Proteomics. Volume 1599, 1-2 (2002): 65-71.

D. Medjahed, T. S. Tontesh, Gary W. Smythers, Brian T. Luke, P. F. Lemkin and D. J. Monroe. "TMAP (Tissue Molecular Anatomy Project)." 2002 Congress of Applied Proteomics. (2002): 71-72.

Igor A. Topol, Stanley K. Burt, E. Deretey, T. H. Tang, A. Perczel, A. Rashin and I. G. Csizmadia. "alpha and 310- Helix Interconversion: A Quantum-Chemical Study on Polyalanine Systems in the Gas Phase and in Aqueous Solvent." Journal of American Chemical Society. Volume 123, 25 (2002): 6054-6060.

Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell FB, White O, and Salzberg SL. "Full-Length Messenger RNA Sequences Greatly Improve Genome Annotation." GenomeBiology. Volume 3, 6a (2002): research29.1-12.

Joseph Ivanic and Klaus Ruedenberg. "Deadwood in Configuration Spaces. II. SD and SDTQ spaces." Theoretical Chemistry Accounts. Volume 4 (2002): 220.

2001

A. A. Rashin, Igor A. Topol, G. J. Tawa and Stanley K. Burt. "Charge Distributions in Water and Ion-Water Clusters." Chemical Physics Letters. Volume 335 (2001): 327-333.

O. N. Ventura , Kieninger M, P.A. Denis and Raul E. Cachau. "Density Functional Computational Thermochemistry: Isomerization of Sulfine and Its Enthalpy of Formation." Journal of Physical Chemistry A. Volume 105, 43 (2001): 9912-9916.

Igor A. Topol, C. McGrath, E. Chertova, C. Dasenbrock, M. R. LaCourse, M. A. Eissenstat, Stanley K. Burt, L. E. Henderson and J. R. Casas-Fine. "Experimental Determination and Calculations of Redox potential Descriptors of Compounds Directed Against Retroviral Zinc Fingers: Implications for Rational Drug Design." Protein Science. Volume 10 (2001): 1434-1445.

Salomon R. Billeter, Simon P. Webb, Pratul K. Agarwal, Tzvetelin Iordinov and Sharon Hammes-Schiffer. "Hydride Transfer in Liver Alcohol Dehydrogenase: Quantum Dynamics, Kinetic Isotope Effects, and the Role of Enzyme Motion." Journal of American Chemical Society. Volume 123 (2001): 11262-11272.

Salomon R. Billeter, Simon P. Webb, Tzvetelin Iordinov, Pratul K. Agarwal and Sharon Hammes-Schiffer. "Hybrid Approach for Including Electronic and Nuclear Quantum Effects in Molecular Dynamics Simulations of Hydrogen Transfer Reactions in Enzymes." Journal of Chemical Physics. Volume 14 (2001): 6925-6936.

Igor A. Topol, A. V. Nemukhin, Y. I. Dobrogorskaya and Stanley K. Burt. "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." Journal of Physical Chemistry B. Volume 45 (2001): 11341-11350.

P. Ordejón, E. Artacho, Raul E. Cachau, J. Gale, A. García, J. Junquera, J. Kohanoff, M. Machado, D. Sanchez-Portal, J. M. Soler and R. Weht. "Linear Scaling DFT Calculations with Numerical Atomic Orbitals." Materials Research Society Symposium. Volume 677, AA9.6 (2001): 1-11.

Tzvetelin Iordinov, Salomon R. Billeter, Simon P. Webb and Sharon Hammes-Schiffer. "Partial Multidimensional Grid Generation Method for Efficient Calculation of Nuclear Wavefunctions." Chemical Physics Letters. Volume 338 (2001): 389-397.

Yuri G. Abashkin, J. W. Erickson and Stanley K. Burt. "Quantum Chemical Investigation of Enzymatic Activity in DNA Polymerase B. A Mechanistic Study." Journal of Physical Chemistry B. Volume 105 (2001): 287-292..

Yuri G. Abashkin, Jack R. Collins and Stanley K. Burt. "The (salen) Mn(III)-catalyzed Epoxidation Reaction as a Multi-channel Process with Different Spin States. Electronic Tuning of Asymmetric Catalysis: a Theoretical Study." Inorg. Chem. Volume 40 (2001): 4040-4048.

Mark S. Gordon, Simon P. Webb, Takako Kudo, Brett M. Bode, Jerzy Moc, Dmitri G. Fedorov and Gyusung Chung. "Titanium Chemistry." Computational Organometallic Chemistry. (2001)

Volfovsky N, Haas BJ, and Salzberg SL. "A clustering method for repeat analysis in DNA sequences." GenomeBiology. Volume 2, 8 (2001): research27.

Joseph Ivanic and Klaus Ruedenberg. "Identification of Deadwood in Configuration Spaces through General Direct Configuration Interaction." Theoretical Chemistry Accounts. Volume 106 (2001): 339.

Sarangan Ravichandran, J.D. Madura and Julian Talbot. "A Brownian dynamics study of the initial stages of Hen-Egg white Lysozyme adsorption at a solid interface." Journal of Physical Chemistry B. Volume 105 (2001): 3610-3613.

2000

Igor A. Topol, G. J. Tawa, R. A. Caldwell, M. A. Eissenstat and Stanley K. Burt. "Acidity of Organic Molecules in the Gas Phase and in Aqueous Solvent." Journal of Physical Chemistry A. Volume 104, 42 (2000): 9619-9624.

Igor A. Topol, Stanley K. Burt, A. A. Rashin and J. W. Erickson. "Calculation of Substitute Effects on pKa Values of Pyrone and Dihydropyrone Inhibitors of HIV-1 Protease." Journal of Physical Chemistry A. Volume 104, 4 (2000): 866-872.

Simon P. Webb, Pratul K. Agarwal and Sharon Hammes-Schiffer. "Combining Electronic Structure Methods with Calculation of Hydrogen Vibrational Wavefunctions: Application to Hydride Transfer Catalyzed by Liver Alcohol Dehydrogenase." Journal of Physical Chemistry B. Volume 104 (2000): 8884-8894.

Pratul K. Agarwal, Simon P. Webb and Sharon Hammes-Schiffer. "Computational Studies of the Mechanism for Proton and Hydride Transfer in Liver Alcohol Dehydrogenase." Journal of American Chemical Society. Volume 122 (2000): 4803-4812.

J. Kohanoff, S. Koval, D. A. Estrin, D. Laria and Yuri G. Abashkin. "Concertedness and Solvent Effects in Multiple Proton Transfer Reactions: the Formic Acid Dimmer in Solution." Journal of Chemical Physics. Volume 112, 21 (2000): 9498-9508.

O. N. Ventura, M. Kieninger, Raul E. Cachau and S. Suhai. "Density Functional Computational Thermochemistry. Determination of the Enthalpy of Formation of Sulfine, CH2=S=O, at Room Temperature." Chemical Physics Letters. Volume 329, 1-2 (2000): 145-153.

Simon P. Webb and Sharon Hammes-Schiffer. "Fourier-Grid Hamiltonian Multiconfigurational Self-Consistent Field: A Method to Calculate Multidimensional Hydrogen Vibrational Wavefunctions." Journal of Chemical Physics. Volume 113 (2000): 5214-5227.

B. L. Grigorenko, A. V. Nemukhin, Igor A. Topol and Stanley K. Burt. "Hydrogen Bonding at the Diatomics-in-Molecule Level: Water Clusters." Journal of Chemical Physics. Volume 113, 7 (2000): 2638-2647.

Raul 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. "Model of the Catalytic Mechanism of Human Aldose Reductase Based on Quantum Chemical Calculations." Journal de Physique IV France. Volume 10 (2000): 3-13.

S.W. Rick and Raul E. Cachau. "The Nonplanarity of the Peptide Group: Molecular Dynamics Simulations with a Polarizable Two-state Model for the Peptide Bond." Journal of Chemical Physics. Volume 112, 11 (2000): 5230-5241.

Igor A. Topol, A. V. Nemukhin, M. Chao, L. K. Iyer, G. J. Tawa and Stanley K. Burt. "Quantum Chemical Studies of Reactions of the Cyclic Disulfides with the Zinc Finger Domains in the HIV-1 Nucleocapsid Protein (NCp7)." Journal of American Chemical Society. Volume 122, 29 (2000): 7087-7094.

G.A. Arteca, Raul E. Cachau and K. Veluri. "Structural Complexity of H-bonded Networks." Chemical Physics Letters. Volume 319, 5-6 (2000): 719-724.

The Arabidopsis Genome Initiative. "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana." Nature. Volume 408 (2000): 796-815.

1999

S. W. Rick, Yuri G. Abashkin, R. Hildebrandt and Stanley K. Burt. "Computational Studies of the Domain Movement and the Catalytic Mechanism of Thymidine Phosphorylase." Proteins: Structure, Function, and Genetics. Volume 37 (1999): 242-252.

Simon P. Webb and Mark S. Gordon. "Intermolecular Self-Interactions of the Titanium Tetrahalides (TiX4, X=F,Cl,Br)." Journal of American Chemical Society. Volume 121 (1999): 2552-2560.

Igor A. Topol, G. J. Tawa, Stanley K. Burt and A. A. Rashin. "On the Structure and Thermodynamics of Solvated Monoatomic Ions Using a Hybrid Solvation Model." Journal of Chemical Physics. Volume 111, 24 (1999): 10998-11014.

Simon P. Webb and Mark S. Gordon. "Solvation of the Menshutkin Reaction: A Rigorous Test of the Effective Fragment Method." Journal of Physical Chemistry A. Volume 103 (1999): 1265-1273.

Volfovsky N, Parnas H, Segal M, and Korkotian E. "Geometry of dendritic spines affects calcium dynamics in hippocampal neurons: theory and experiments." J Neurophysiology. Volume 82, 1 (1999): 450-62.

Ravin R, Parnas H, Spira ME, Volfovsky N, and Parnas I. "Simultaneous measurement of evoked release and [Ca++]i in crayfish release bouton reveals high affinity of release to Ca++." J Neurophysiology. Volume 81, 2 (1999): 634-42.

1998

G. J. Tawa, Igor A. Topol, Stanley K. Burt, R. A. Caldwell and A. A. Rashin. "Calculation of the Aqueous Solvation Free Energy of the Proton." Journal of Chemical Physics. Volume 109 (1998): 4852-4863.

G. J. Tawa, Igor A. Topol, Stanely K. Burt and J. W. Erickson. "Calculation of Relative Binding Free Energies of Peptidic Inhibitors to HIV-1 Protease and its I84V Mutant." Journal of American Chemical Society. Volume 120, 34 (1998): 8856-8863.

Jack R. Collins, X. Luo and R. Kato. "Dynamic Flexibility of Protein-Inhibitor Complexes. A Study of the HIV-1 Protease/KNI-272 Complex." Journal of American Chemical Society. Volume 120 (1998): 12410-12418.

Simon P. Webb and Mark S.Gordon. "The Effect of Spin-Orbit Coupling on the Magnetic Properties of Ti2H6." Journal of Chemical Physics. Volume 109 (1998): 919-927.

Simon P. Webb and Mark S. Gordon. "Molecular Electronic Structure and Energetics of the Isomers of Ti2H6." Journal of American Chemical Society. Volume 120 (1998): 3846-3857.

Raul E. Cachau and Yuri G. Abashkin. "Proline Cis-Trans Isomerization in Cyclophilin: a One Step Catalytic Mechanism Revealed by a Combined Free Energy Perturbation and Density Functional Study." The Molecular Modeling E-Conference 1997-1998. Volume 2 (1998)

Igor A. Topol, J. R. Casas-Finet, R. Gussio, Stanley K. Burt and J. W. Erickson. "A Quantum-Mechanical Study of Metal Binding Sites in Zinc Finger Structures." Journal of Molecular Structure. Volume 423, 1-2 (1998): 13-28.

Anders S. Wallqvist, Gary W. Smythers, and David G. Covell. "A cooperative folding unit in HIV-1 protease. Implications for protein stability and occurrence of drug-induced mutations." Protein Eng.. Volume 11 (1998): 999-1005.

1997

L. Young, Igor A. Topol, Stanley K. Burt and A. A. Rashin. "Building Molecular Charge Distributions from Fragments: Application to HIV-1 Protease Inhibitors." Journal of Computational Chemistry. Volume 18, 4 (1997): 522-532.

Igor A. Topol, G. J. Tawa, Stanley K. Burt and A. A. Rashin. "Calculation of Absolute and Relative Acidities of Substituted Imidazoles in Aqueous Solvent." Journal of Physical Chemistry A. Volume 101, 51 (1997): 10075-10081.

Yuri G. Abashkin, Stanley K. Burt and N. Russo. "Density Functional Study of the Mechanisms and the Potential Energy Surfaces of MCH2+ + H2 Reactions. The Case of Cobalt and Rhodium (M=Co,Rh)." Journal of Physical Chemistry A. Volume 101 (1997): 8085-8093.

S. V. Gulnik, L. I. Suvorov, P. Majer, Jack R. Collins, B. P. Kane, D. G. Johnson and J.W. Erickson. "Design of Sensitive Fluorogenic Substrates for Human Cathespin D." FEBS Letters. Volume 413 (1997): 379-384.

Morris Krauss and Simon P. Webb. "Solvation and the Excited States of Formamide." Journal of Chemical Physics. Volume 107 (1997): 5771-5775.

P. Majer, Jack R. Collins, S. V. Gulnik and J. W. Erickson. "Structure-based Subsite Specificity Mapping of Human Cathepsin D Using Statine-Based Inhibitors." Protein Science. Volume 6 (1997): 1458-1466.

Anders S. Wallqvist, Gary W. Smythers, and David G. Covell . "Identification of cooperative folding units in a set of native proteins." Protein Science. Volume 6 (1997): 1627-1642.

1996

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. "An Effective Fragment Method for Modeling Solvent Effects in Quantum Mechanical Calculations." Journal of Chemical Physics. Volume 105 (1996): 1968-1986.

N. Russo, Yuri G. Abashkin, P. Calaminici, T. Mineva, E. Sicilia and M. Toscano. "Gaussian Density Functional Method: an Alternative Tool for the Prediction of Physico-chemical Properties." World Scientific Publishing Company. (1996): 100-121.

G. Frenking, S. Dapprich, K. F. Kohler, W. Koch and Jack R. Collins. "Structure and Bonding of the Remarkable Donor-acceptor Compelxes XBeO (X=NH3, NMe3, CO, N2, C2H2, C2H4, H2, H2CO, O2)." Molecular Physics. Volume 89 (1996): 1245-1263.

A. Silva, A. Y. Lee, S. V. Gulnik, P. Majer, Jack R. Collins, T. N. Bhat, P. J. Collins, Raul E. Cachau, K. E. Luker, I. Y. Gluzman, S. E. Francis, A. Oksman, D. E. Goldberg and J. W. Erickson. "Structure and Inhibition of Plasmepsin II, a Hemoglobin-degrading Enzyme from Plasmodium Falciparum." National Academy Science. Volume 93 (1996): 10034-9.

1995

Jack R. Collins, Stanley K. Burt and J. W. Erickson. "Activated Dynamics of Flap Opening in HIV-1 Protease." Advances in Experimental Medicine and Biology. Volume 362 (1995): 455-460.

Yuri G. Abashkin, N. Russo, E. Sicilia and M. Toscano. "Constrained Optimization Procedure for Finding Transition States and Reaction Pathways in the Framework of Gaussian Based Density Functional Method." Modern Density Functional Theory: A Tool for Chemistry. Theoretical and Computational Chemistry. Volume 2 (1995): 255-272.

Yuri G. Abashkin, Stanley K. Burt, Jack R. Collins, Raul E. Cachau, N. Russo and J. W. Erickson. "Density Functional Modeling of Ligand-metal Interactions and Enzymatic Activities in Metalloenzymes. Peptide Bond Cleavage by Carboxypeptidase A." Metal-ligand Interactions - Structure and Reactivity. (1995): 1-22.

Simon P. Webb and Mark S. Gordon. "The Dimerization of TiH4." Journal of American Chemical Society. Volume 117 (1995): 7195-7201.

Jack R. Collins, Stanley K. Burt and J. W. Erickson. "Flap Opening in HIV-1 Protease Simulated by 'Activated' Molecular Dynamics." National Structural Biology. Volume 2 (1995): 334-8.

Yuri G. Abashkin, N. Russo and M. Toscano. "Transition States Localization by Density Functional Method. Applications to Isomerization and Symmetry-forbidden Reactions." Theoretical Chemistry Accounts. Volume 19 (1995): 179-186.

1994

Yuri G. Abashkin, F. Mele, N. Russo and M. Toscano. "Density Functional Treatment of Water-carbon Dioxide Van Der Waals Complex." International Journal of Quantum Chemistry. Volume 52 (1994): 1011-1015.

J. A. Fruetel, Y. T. Chang, Jack R. Collins, G. H. Loew and P.R. Ortiz de Montellano. "Thioanisole Sulfoxidation by Cytochrome P450cam (CYP101)." Journal of American Chemical Society. Volume 116 (1994): 11643-8.

Yuri G. Abashkin and N. Russo. "Transition State Structures and Reaction Profiles Form Constrained Optimization Procedure. Implementation in the Framework of Density Functional Theory." Journal of Chemical Physics. Volume 100 (1994): 0.

Yuri G. Abashkin, N. Russo and M. Toscano. "Transition States and Energy Barriers From Density Functional Studies: Representative Isomerization Reactions." International Journal of Quantum Chemistry. Volume 52 (1994): 695-704.

David G. Covell, Gary W. Smythers, A. M. Gronenborn,. "Analysis of Hydrophobicity in the Alpha and Beta Chemokine Families and its Relevance to Dimerization." Protein Science. Volume 3 (1994): 2064-2072.

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