Publications

2006:

  • Deerfield II, D.W., Davis, C.H., Wymore, T, Stafford, D.W., Pedersen, L.G. 2006. A Quantum Chemical Study of the Mechanism of action of Vitamin K Epoxide Reductase (VKOR) Int. J. Quantum Chem., accepted.

  • Davis, C.H., Deerfield II, D.W., ,Wymore, T, Stafford, D.W., Pedersen, L.G. 2006. A Quantum Chemical Study of the Mechanism of action of Vitamin K Epoxide Reductase (VKOR) II.Transition States. Int. J. Quantum Chem., submitted.

  • Deerfield, D., Hood, G. 2006. An Experiment in Using the Access Grid for Distance Education. Journal of Science Education and Technology. Journal of Science Education and Technology. submitted.

  • Deerfield II, D.W., Wymori, T., Pedersen, L.G.. 2006. Comparison of the Binding of Monoalkyl and Dialkyl Phosphates with Divalent Metal Ions: A Quantum Mechanical Study. Manuscript in preparation.

    • 2005:

  • Nicholasi Jr., H B., Deerfield, D. W., Ropelewski, A.J.. 2005. Bioinformatics for Sequence and Genomic Data in press.

    • 2004:

  • Nicholas, H. B., Wymore, T., Cho, S. S., MacKerell, A. D., Deerfield, D. W.. 2004. Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophilic activation. Proteins Structure Function Bioinformatics. 57:758-771.

  • Wymore, T., Hempel, J., Cho, S.S., MacKerrell Jr, A.D., Nicholas Jr., H.B., Deerfield II, D.W. 2004. Molecular Recognition of Aldehydes by Aldehyde Dehydrogenase and Mechanism of Nucleophile Activation Proteins, 57(4): 758-771. Entrez Entry

  • Brothers EN, Suarez D, Deerfield DW II, Merz KM Jr. 2004. PM3-compatible zinc parameters optimized for metalloenzyme active sites. J Comput Chem., 25(14):1677-92. Entrex Entry

  • Ropelewski, A.J., Nicholas, H.B. Jr, Deerfield, D.W. II, 2004. "Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch", in Current Protocols in Bioinformatics, Volume I, Baxevanis, A., and Davison, D. ed., pp 3.10.1 - 3.10.13

    • 2003:

  • Wetzel, A.W., Nieder, G.L., Durka-Pelok, G. Gest, T.R., Pomerantz, S.M. Nave, D., Czanner, S., Wagner, L., Shirey, E., Deerfield II, D.W. 2003. Photo-Realistic Representation of Anatomical Structures for Medical Education by Fusion of Volumetric and Surface Image Data Proceedings of 32nd Applied Imagery and Pattern Recognition Workshop: Image Data Fusion, Oct 15-17 2003, Washington DC, IEEE Computer Society Press, pp 131-138.

  • Nicholas, H.B. Jr., Deerfield, D.W. II, Ropelewski, A.J. 2003. Strategies for Searching Sequence Databases in "Biocomputing: Computer Tools for Biologists", Eaton Publishing, ed. S.M.Brown., pp 209-231..

  • Wymore, T., Deerfield II, D.W., Field, M.J., Nicholas, H.B. Hempel, J.. 2003. Initial Events in class 3 Aldehyde Dehydrogenase: MM and QM/MM simulations Chemico-Biological Interactions, 2003, 143-144: 75-84. Entrez Entry

    • 2002:

  • Nicholas Jr., H.B., Ropelewski, A.J., Deerfield II, D.W. 2002. Strategies for Multiple Sequence Alignment. Biotechniques, 32:592-603. Entrez Entry

  • Wetzel, A.W., Pomerantz, S.M., Nave, D., A. Kar, Sommerfield, J., Mathis, M., Deerfield II, D.W., Bookstein, F.L., Green, W.D., Ade, A., Athey, B.. 2002. A Networked Environment for Interactively Viewing and Manipulating Visible Human Datasets, Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19.

  • Pomerantz, S.M., Wetzel, A.W., Nave, D., Deerfield II, D.W.. 2002. A Natural Plane Anatomical Segmentation Interface, Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19.

  • Nave, D., Pomerantz, S.M., Wetzel, A.W., Deerfield II, D.W.. 2002. Semi-Automated Reconstruction of Biological Surfaces from Few Contours in the Visible Female Dataset, Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19.

    • 2001:

  • Wagner, M.H., Tsui, F.-C., Espino, J.U., Dato, V.M., Sittig, D.F., Caruana, R.A., McGinnis, L.F., Deerfield, D.W. Druzdzel, M.J., and Fridsma, D.B. 2001. The Emerging Science of Very Early Detection of Disease Outbreaks J. Public Health Management Practice 7:51-59. Entrex Entry

  • Deerfield II, D.W., Carter Jr, C.W., Pedersen, L.G. 2001. Models for Protein-Zinc Ion Binding Sites II: The Catalytic Sites. Int. J. Quantum Chem. 83:150-165.

    • 2000:

  • Crowley, M.F. Deerfield II, D.W.. Darden, T.A. Cheatham III, T.E. 2000. Molecular Dynamics Simulations using Particle-Mesh Ewald Methods. in Parallel Computing for Industrial Applications, Koniges, A. (Ed), Morgan Kaufmann, 355-387.

  • Ropelewski, A.J., Nicholas Jr., H.B., Deerfield II, D.W. 2000. Selective and Sensitive Comparison of Genetic Sequence Data on High Performance Computers. in Parallel Computing for Industrial Applications, Koniges, A. (Ed), Morgan Kaufmann, 453-479.

  • Nicholas, H.B. Jr., Deerfield, D.W. II, Ropelewski, A.J. 2000. Strategies for Searching Sequence Databases Biotechniques 28:1174-1191. Entrez Entry

  • Tiraboschi, G., Gresh, N., Giessner-Prettre, C., Pedersen, L.G., Deerfield, D.W. II. 2000. A joint ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands. Variations of the binding energy and of its components with the number and the charges of the ligands. J. Comp. Chem. 21:1011-1039.

    •

    1999:

  • Welling, J., Foss, G., Deerfield II, D.W.. 1999. The Biomedical Supercomputing Initiative at the Pittsburgh Supercomputing Center. sigbio newsletter 19:17-19.

    • 1998:

  • Wetzel, A.W., Crowley, R., Dawson, R., Gilbertson, J., Kim, S.J., Yagi, Y., Zheng, L., Gadd, C., Joo, Y.M., Deerfield, D.W., and Becich, M.J. "Evaluation of prostate tumor grades by content based image retrieval" 27th Applied Imagry and Pattern Workshop: Advances in Computer Assisted Recognition Washington D.C., Oct 16, 1998, and SPIE Proceedings volume 3584, pages 244-252, 1998.

    • 1997:

  • Deerfield II, D.W., Holland-Minkley, A.M., Geigel, J., Nicholas Jr., H.B.. 1997. Classification of the Environment of Protein Residues J. Prot. Chem. 16:441-446. Entrez Entry

  • Nicholas, K.B., Nicholas Jr., H.B., Deerfield II, D.W.. 1997. GeneDoc: Analysis and Visualization of Genetic Variation EMBNET.NEWS 4:1-4.

  • Ropelewski, A.J., Nicholas Jr., H.B., Deerfield II, D.W.. 1997. Implementation of Genetic Sequence Alignment Programs on Supercomputers J. Supercomputing 11:237-253.

  • Crowley, M.F., Darden, T., Cheatham, T. Deerfield II, D.W.. 1997. Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program. J. Supercomputing 11:255-278.

  • Deerfield II, D.W., Pedersen, L.G.. 1997. Structure and Relative Acidity for a Zinc Finger J. Mol. Struct. (THEOCHEM) 419:221-226.

    • 1996:

  • Deerfield II, D.W., Pedersen, L.G.. 1996. Enol and Deprotonated Forms of Acetic and Malonic Acid J. Mol. Struct. (THEOCHEM) 368:163-196.

    • 1995:

  • Deerfield II, D.W., Fox, D.J., Head-Gordon, M., Hiskey, R.G., Pedersen, L.G.. 1995. The First Solvation Shell of Magnesium Ions in a Model Protein Environment with Formate, Water and X=NH3, H2S, Imidazole, Formaldehyde and Chloride as Ligands: An ab initio Study. Proteins 21:244-255. Entrez Entry

  • Cabaniss, S., Deerfield II, D.W., Monroe, D.M., Hiskey, R.G., Pedersen, L.G.. 1995. Is Ca(II) ion binding to Prothrombin Fragment 1 Intrinsically Cooperative or is Cooperative Binding Accounted for by Self Association? Blood Coagulation Fibrinolysis 6:464-473. Entrez Entry

  • Nicholas Jr., H.B., Ropelewski, A.J., Deerfield II, D.W., Behrmann, J.G.. 1995. A Metric Measure for Comparing Sequnec Alignments in Methods in Protein Sequence Analysis, Plenum Press, NY, eds. M.Z. Atassi, E. Appella, 515-525.

  • Deerfield II, D.W., Pedersen, L.G.. 1995. The First Solvation Shell of Magnesium Ions in a Model Nucleic Acid Environment: An ab initio Study. J. Biomol. Struct. Dynam. 13:167-180. Entrez Entry

  • Deerfield II, D.W., Pedersen, L.G.. 1995. An ab initio Quantum Mechanical Study of Thioesters. J. Mol. Struct. (THEOCHEM) 358:99-106.

    • 1994:

  • Deerfield II, D.W., Holland-Minkley, A., Hempel, J.D., Nicholas Jr., H.B.. 1994. Conformational Flexibility of the Gly-Gly dipeptide within protein structures. J. Protein. Chem. 13:526.

  • Nicholas, H., Hempel, J., Hinich, A., Deerfield, D., Behrman, J. Ropelewski, A.. 1994. Quantative Evaluation of different Multiple Alignment Programs J. Protein. Chem. 13:534.

    • 1993:

  • Shuey, S.W., Deerfield II, D.W., Amburgey, J.C., Cabaniss, S.E., Huh, N.-W., Charifson, P.S., Pedersen, L.G., Hiskey, R.G.. 1993. Cyclohexanediol Biphosphates as Models for Phospholipid-Metal Ion Binding Sites. Bioorganic Chemistry, 21:95-108.

    • 1992:

  • York, D.M., Darden, T., Deerfield II, D.W., Pedersen, L.G.. 1992. The Interaction of Na(I), Ca(II) and Mg(II) Metal Ions with Duplex DNA. Int. J. Quantum Chem: Biol. Symp, 19:145-166.

    • 1991:

  • Deerfield II, D.W., Fox, D.J., Head-Gordon, M., Hiskey, R.G., Pedersen, L.G.. 1991. The Interaction of Calcium and Magnesium Ions with Malonate and the Role of the Waters of Hydration: A Quantum Mechanics Study. J. Am. Chem. Soc., 113:1892-1899.

  • Monroe, D.M., Deerfield II, D.W., , Olson, D.L., Stewart, T.N., Treanor, R.E., Roberts, H.R., Hiskey, R.G., Pedersen, L.G.. 1991. Calcium Ion binding to Human and Bovine Factor X. Blood Coagulation and Fibrinolysis, 1:633-640. Entrez Entry

  • Smith, P.R., Ropelewski, A.J., Balog, D.A., Gottesman, Deerfield II, D.W.. 1991. A Simple Approach for the Distribution of Computationally Intense Tasks in an Heterogeneous Environment: Distribution of the MDPP Image Processing Package. CABIOS, 7:501-507. Entrez Entry

    • 1990:

  • Cain, J.T., Deerfield II, D.W., Hiskey, R.G., Pedersen, L.G.. 1990. The Divalent Metal Ion Mediated Interaction of Proteins with Negatively Charged Membranes: A Model Study Employing Molecular Mechanics. Int. J. Peptide Protein Res., 35:111-116. Entrez Entry

  • Lapadat, M.A., Deerfield II, D.W., Pedersen, L.G. Spremulli, L.L.. 1990. Generation of Potential Structures for the G-Domain of Chloroplast EF-Tu(CHL) using Comparative Molecular Modeling. Proteins, 8:237-250. Entrez Entry

    • 1989:

  • Deerfield II, D.W., Lapadat, M.A., Spermulli, L.L., Hiskey, R.G., Pedersen, L.G.. 1989. The Role of Hydrated Divalent Metal Ions in the Bridging of Two Anionic Groups. An ab initio and Molecular Mechanics Study of Dimethyl Phosphate and Formate Bridged by Calcium and Magnesium Ions. J. Biomolecular Stereo Dynamics 6, 1077-1091. Entrez Entry

  • Deerfield II, D.W., Nicholas, H.B., Jr., Hiskey, R.G., Pedersen, L.G.. 1989. Salt or Ion Bridges in Biological Systems: A Study Employing Quantum and Molecular Mechanics. Proteins 6, 168-192. Entrez Entry

    • 1988:

  • Maynard, A.T., Eastman, M.A., Darden, T., Deerfield II, D.W., Hiskey, R.G., Pedersen, L.G.. 1988. The Effect of Calcium(II) and Magnesium(II) Ions on the 18-23 (gamma)-Carboxyglutamic Acid containing Cyclic Peptide Loop of Bovine Prothrombin: An AMBER Molecular Mechanics Study. Int. J. Peptide Protein Res. 31:137-149. Entrez Entry

  • Lewis, M.L., Deerfield II, D.W., Hoke, R.A., Koehler, K.A., Pedersen, L.G., Hiskey, R.G.. 1988. Studies on Ca(II), Mg(II) Binding to (gamma)-Carboxyglutamic Acid. Use of Thermal Decarboxylation to Probe Metal Ion/GLA Interactions. J. Biol. Chem. 263:1358-1363, 1988. Entrez Entry

  • Zapata, G.A., Berkowitz, P., Noyes, C.M., Pollock, J.S., Deerfield II, D.W., Pedersen, L.G., Hiskey, R.G.. 1988. Chemical Modification of Bovine Prothrombin Fragment 1 in the Presence of Tb(III) Ions. Sequence Studies on Bovine 3-(gamma)-M-Glu-Fragment 1. J. Biol. Chem. 263:8150-8156. Entrez Entry

  • Pedersen, L.G., Darden, T., Deerfield II, D.W., Anderson, M., Hoel, D.. 1988. A Theoretical Study of the Effect of Methylation or Ethylation at O6-Guanine on the Structure and Energy of DNA Double Strands. Carcinogenesis 9:1553-1562. Entrez Entry

    • 1987:

  • Olson, D.L., Deerfield II, D.W., Berkowitz, P., Hiskey, R.G., Pedersen, L.G.. 1987. Determination of Magnesium Binding to Macromolecules. Anal. Biochem. 160:468-470. Entrez Entry

  • Deerfield II, D.W., Olson, D.L., Berkowitz, P., Byrd, P.A., Koehler, K.A., Pedersen, L.G., Hiskey, R.G.. 1987. Mg(II) Binding by Bovine Prothrombin Fragment 1 via Equilibrium Dialysis and the Relative Roles of Mg(II) and Ca(II) in Blood Coagulation. J. Biol. Chem. 262:4017-4023. Entrez Entry

  • Deerfield II, D.W., Olson, D.L., Berkowitz, P., Pedersen, L.G., Koehler, K.A., Hiskey, R.G.. 1987. Relative Affinity of Ca(II) and Mg(II) Ions for Human and Bovine Prothrombin and Fragment 1. Biophys. Bioorg. Res. Comm. 144:520-527. Entrez Entry

  • Yokomori, Y., Deerfield II, D.W., Olson, D.L., Berkowitz, P., Pedersen, L.G., Koehler, K.A. Hiskey, R.G.. 1987. Conformation and Structure of a Blocked Gla Residue: N-Benzyloxycarbonyl-((gamma),(gamma),Di-tert-(Butyl)-)-L-(gamma)- Carboxyglutamic Acid (alpha)-Methyl Ester. Acta Cryst. C43:1567-1569.

  • Pollock, J.S., Zapata, G.A., Weber, D.J., Berkowitz, P., Deerfield II, D.W., Olson, D.L., Koehler, K.A., Pedersen, L.G., Hiskey, R.G.. 1987. Studies on the Metal Ion-Binding of the Bovine Prothrombin Gla Domain to Phospholipid Vesicles. in "Current Advances in Vitamin K Research, A Steenbock Symposium", Elsevier Science Publishing Co., Inc., ed. John W. Suttle, pp 325-344.

    • 1986:

  • Deerfield II, D.W., Berkowitz, P., Olson, D.L., Wells, S., Hoke, R.A., Koehler, K.A., Pedersen, L.G., Hiskey, R.G.. 1986. The Effect of Divalent Metal Ions on the Electrophoretic Mobility of Bovine Prothrombin and Bovine Prothrombin Fragment 1. J. Biol. Chem. 261:4833-4839. Entrez Entry

  • Wright, S.F., Berkowitz, P., Deerfield II, D.W., Byrd, P.A., Olson, D.L., Larson, R.S., Hinn, G.C., Koehler, K.A., Pedersen, L.G., Hiskey, R.G.. 1986. Chemical Modification of Bovine Prothrombin Fragment 1 in the Presence of Tb(III) Ions. J. Biol. Chem. 261:10598-10605. Entrez Entry

  • Marsh, H.C., Hoke, R.A., Deerfield II, D.W., Pedersen, L.G., Hiskey, R.G., Koehler, K.A.. 1986. Terbium Ion Binding to a Synthetic (gamma)-Carboxyglutamic Acid Containing Heptapeptide corresponding to Bovine Prothrombin Residues 17-23. Inorg. Chem. 25:4503-4506.

  • Deerfield II, D.W., Hoke, R.A., Darden, T., Pedersen, L.G., Hiskey, R.G.. 1986. Relative Spectral Response as a Function of Sequential Ligand Binding. Biophys. Bioorg. Res. Comm. 141:1207-1212. Entrez Entry

  • Hoke, R.A., Deerfield II, D.W., Koehler, K.A., Hiskey, R.G.. 1986. Synthesis of a (gamma)-Carboxyglutamic Acid Containing Heptapeptide Corresponding to Bovine Prothrombin Residues 17-23. Int. J. Peptide Protein Res. 28:569-578. Entrez Entry

    • 1985:

  • Gray, A.L., Hoke, R.A., Deerfield II, D.W., Hiskey, R.G.. 1985. Side Chain Interactions Between Arginine and (gamma)-Carboxyglutamic Acid. Studies on the Decarboxylation of (gamma)-Carboxyglutamic Acid in the Presence of Arginine. J. Org. Chem. 50:2189-2191.

    • 1981:

  • Dixon, D.A., Deerfield II, D.W., Grahm, G.D. 1981. The Electronic Structure of Dodecahedrane and the Nature of the Central Cavity. Chem. Phys. Lett. 78:161-164.

    • Invited Talks and Lectures

    2003:

  • A Bioinformatics and Computational Chemistry Study of Binding of Divalent Metal Ions to Biopolymers Distinguished Lecture Series in Bioinformatics, University of Pittsburgh, February 5, 2003.
  • Approaches Towards Whole genome Annotation. University of Texas at San Antonio, March 7, 2003.
  • Navigating through Large 3D Volumetric Datasets: Application to the Visible Human. Louisiana State University, March 18, 2003.
  • Navigating through Large 3D Volumetric Datasets: Application to the Visible Human. Albert Einstein College of Medicine, April 3, 2003.

    • 2002:

  • An Overview of Bioinformatics and Computational Biology University of Puerto Rico at Cayey, October 28, 2002.
  • An Overview of Computational Biology University of Puerto Rico at Mayaguez, October 29, 2002.
  • An Overview of Bioinformatics and Computational Biology University of Puerto Rico Medical Sciences Campus, October 30, 2002.
  • Computational Biology: Research Tools for the Future University of Puerto Rico - Rio Piedras, October 31, 2002.

    • 2001:

  • Protein-Metal Ion Sites and the Relationship to Structure. St. Jude's Children's Research Hospital, Memphis, TN, February 28, 2001.
  • Protein-Metal Ion Sites and the Relationship to Structure. University of Pittsburgh Medical Center, Pittsburgh, PA, March 14, 2001.
  • Sensitive and Selective Searches of Bioinformatics Databases at the University of Idaho in the Bioinformatics Initiative Seminar Series, Moscow, ID, March 30, 2001.

    • 2000:

  • Protein-Metal Ion Sites and the Relationship to Structure. University of Puerto Rico, Medical Sciences Campus, February 3, 2000.

    • 1999:

  • Protein-Metal Ion Sites and the Relationship to Structure. Northwestern University Medical School, Department of Molecular Pharmacology and Biological Chemistry, Chicago, IL, February 15, 1999.
  • Computational Insights into the Role of Metal Ions in Biological Systems DuPont Ag Division, Newark, DE, December 7, 1999.

    • 1998:

  • Chemsitry Resources on the Internet. Short Course at PittCon, Atlanta, GA, March 1, 1998.
  • Sequence-Structure Alignment and the Role of Metal Ions in Stablizing Protein Structures University of Texas - Southwestern, Department of Biochemistry, Dallas, TX. May 11, 1998.
  • Computational Insights into the Role of Metal Ions in Biological Systems NIOSH, Morgantown, WV, June 25, 1998.
  • Computational Insights into the Role of Metal Ions in Biological Systems Hershey Medical Center, Department of Biochemistry, Hershey, PA, August 19, 1998.
  • Computational Structural Biology: Sequence-Structure Alignment NMHCC's 2nd International Conference on Protein Analysis and Characterization, Wyndham Franklin Plaza Hotel, Philadelphia, PA, December 18, 1998.
  • Protein-Metal Ion Sites and the Relationship to Structure, Lawrence-Berkeley Laboratory, Berkeley, CA., Dec 14, 1998.

    • 1997:

  • Computational Structural Biology: Inverted Structure Prediction. Cornell Theory Center, Ithaca, NY. March 21, 1997.
  • Models for Protein Metal Ion Binding Sites. KECK Institute of Computational Biology, Baylor College of Medicine, April 8, 1997.
  • Computational Structural Biology: Inverted Structure Prediction. NIOSH, Morgantown, WV. September 19, 1997.
  • Computational Structural Biology: Inverted Structure Prediction. Bioinformatics
    San Diego, CA. October 1, 1997.
  • Computational Structural Biology: Inverted Structure Prediction. Protein Analysis and Characterization. New Techniques for Targeting and Drug Discovery. Philadelphia, PA. October 29, 1997.
    •

    1996:


  • Chemsitry Resources on the Internet. Short Course at PittCon, Chicago, IL, March 3, 1996.
  • Computing Resources on the Internet. WVU Conference on Collaboratories
    Morgantown, WV. March 30, 1996.
  • Classification of the Environment of Protein Residues. XIth International Conference on Methods in Protein Structure Analysis. Annecy, France, Sept 4, 1996.

    • 1995:


  • Models for Protein Metal Ion Binding Sites. Department of Chemistry, Washington State University, April 4, 1995.
    • deerfiel@psc.edu (last updated Fri May 1 10:56:34 EDT 1998 )
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