Laboratory of Computational Technologies

Computational tools for data mining and new drug discovery are being developed within our laboratory. These tools are designed to exploit the existing and newly generated databases for the purpose of cancer drug discovery.

Scientific Research Interests: The enormous expansion of new data in the post-genomic data is anticipated to revolutionize the future of biological research and modern medicine. Accompanying this trend is the need to develop advanced computational tools for methods of data analysis and formulation of new experimental designs. Computer-supported analytical techniques combined with interactive and dynamic data visualization tools will be needed to assist in the goals of discovery, decision making and explanation. Our research proposes applications of existing, and construction of newly developed, computational tools for examinations of available databases generated from the bioinformatics sub-fields of proteomics, chemoinformatics and structural genomics. This synthesis will provide an in silico tool for basic research aimed at the discovery, retreival and analysis of relationships between chemical structure, high-throughput screening experiments, molecular target surveys, expression datasets and mutational experiments.

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Group Members: Anders Wallqvist Narmada Thanki

Credentials

David Covell received his academic training at the University of Michigan, with degrees in Aerospace Engineering (B.S.E.), Computer Science(M.S.E.) and Bioengineering(Ph.D.). He came to the National Cancer Institute as a Staff Fellow in the Laboratory of Computational and Experimental Biology, where, under the mentorship of Dr. Mones Berman, he applied mathematical modeling techniques to a wide range of clinical questions. As a Principal Investigator in the NCI, his research interests expanded into areas of computation molecular biology and drug discovery. His current research interests involve the development of computational tools for novel drug discoveries.

Recent Publications

NCBI PubMed listing of publications by David Covell.

Keskin O, Ji X, Blaszcyk J, Covell DG. Molecular motions and conformational changes of HPPK Proteins. 2002 Nov 1;49(2):191-205.

Stephen AG, Worthy KM, Towler E, Mikovits JA, Sei S, Roberts P, Yang QE, Akee RK, Klausmeyer P, McCloud TG, Henderson L, Rein A, Covell DG, Currens M, Shoemaker RH, Fisher RJ. Identification of HIV-1 nucleocapsid protein: nucleic acid antagonists with cellular anti-HIV activity. Biochem Biophys Res Commun. 2002 Sep 6;296(5):1228-37.

Keskin O, Durell SR, Bahar I, Jernigan RL, Covell DG. Relating molecular flexibility to function: a case study of tubulin. Biophys J. 2002 Aug;83(2):663-80.

Bai R, Covell DG, Liu C, Ghosh AK, Hamel E. (-)-doliculide, a new macrocyclic depsipeptide enhancer of actin assembly. J Biol Chem. 2002 Aug 30;277(35):32165-71.

Wallqvist, A., Rabow, A. A., Shoemaker, R. H., Sausville, E. A, Covell D. G.: Establishing connections between microarray expression data and chemotherapeutic cancer pharmacology. Molecular Cancer Ther. 2002 Mar; 1(5):311-20.

Rabow, A. A., Shoemaker, R. H., Sausville, E. A, Covell D. G.: Mining the National Cancer Institute's tumor-screening database: identification of compounds with similar cellular activities. J Med Chem. 2002 Feb 14;45(4):818-40.

Maynard, A. T. and Covell, D.G.:Reactivity of Zinc Finger Cores (I): Analysis of Protein Packing and Electrostatic Screening., J Am Chem Soc 2001 Feb 14;123(6):1047-58.

Bai, R., Covell, D. G., Pei, X-F, Ewell, J. B., Nguyen, N. Y., Brossi, A. and Hamel, E.: Mapping the binding site of colchicinoids on beta-tubulin: 2-chloroacetyl-2-demethylthiocolchicine covalently reacts predominately with cysteine 239 and secondly with cysteine 354, J Biol Chem. 2000 Dec 22;275(51):40443-52.

Keskin, O., Bahar, I., Jernigan, R. L., Beutler, J. A., Shoemaker, R.A., Sausville, E. A. and Covell, D.G.: Characterization of Anticancer Agents by Their Growth-Inhibitory Activity and Relationships to Mechanism of Action and Structure., Anticancer Drug Discovery, 15, 79-98, 2000.

Turpin, J. A., Song, Y., Inman, J.K., Huang, M., Wallqvist, A., Maynard, A., Covell, D. G., Rice, W. A. and Appella, E.: Synthesis and Biological Properties of Novel Pyridinioalkanoyl Thioesters ({PATE}) as Anti-{HIV}-1 Agents that Target the Viral Nucleocapsid Protein Zinc, J. Med. Chem., 42:67-86, 1999.

Maynard, A., Huang, M., Rice, W. G. and Covell, D. G.: Reactivity of the {HIV}-1 {NC}p7 zinc finger domains from the perspective of density-functional theory., Proceeding of the National Academy of Science, 95, 11578-11583, 1998.