JARROD A. SMITH

TSRI TPC15
10550 N. Torrey Pines Rd.
La Jolla, CA 92037
(619)-784-9620
jsmith@scripps.edu

OBJECTIVE

Pursue a career in the development and application of tools for understanding biological systems utilizing modern computer technologies.

EXPERIENCE

1992-1999 : The Scripps Research Institute, La Jolla, CA

Graduate Student, joint advisors David A. Case and Walter J. Chazin

• Solved three-dimensional structures of drug-DNA complexes in solution via NMR spectroscopy and state of the art computer hardware and software.
• Developed new methodologies for refinement and selection of nucleic acid NMR structure ensembles focusing on thorough sampling of conformational space and careful selection of a statistically relevant population.
• Developed a novel molecular dynamics docking method for structure refinement and modeling of dimeric macromolecular systems. Oversaw the successful application of this method to determine solution structures of various drug-DNA, protein-protein, and protein-DNA complexes.
• Wrote numerous innovative pieces of software used by several research groups for the analysis, visualization, and determination of various macromolecular structures.
• Trained and supervised a number of graduate and post-doctoral scientists in the methodologies of NMR data analysis and structure refinement.

1997-1999 : Nanogen, Inc., San Diego, CA

Consultant

• Developed web-browser based tools to interface with in-house proprietary genetic sequence search and analysis software utilizing advanced elements of HTML, CGI, and Perl.
• Installed, configured, and managed UNIX-based http server software.

1992 : Molecular Simulations, Inc., Waltham, MA

Consultant

• Demonstrated the Quanta/CHARMm molecular modeling package to customers in the US and Asia.

1991-1992 : University of California Santa Barbara

Undergraduate Research Assistant, advisor J.T. Gerig

• Described the conformation of an HIV tat peptide in solution utilizing 2D homonuclear 1H NMR techniques.
• Built molecular models of human carbonic anhydrase bound by sulfonamide inhibitors utilizing the Quanta/CHARMm suite.

1989-1991 : University of California Santa Barbara

Undergraduate Research Assistant, advisor R.J. Watts

• Measured excited state lifetimes of organometallic Ruthenium and Iridium complexes with fluorescence laser spectroscopy.
• Synthesis of various substituted phenylpyridines and incorporation of these compounds into Iridium complexes.

EDUCATION

1992-1999 The Scripps Research Institute

• Ph.D., Macromolecular and Cellular Structure and Chemistry.

• B.Sc., Chemistry; with Honors.

PROFESSIONAL SKILLS

• Advanced computing skills under multiple operating environments including UNIX (SunOS, Solaris, HPUX, OSF, IRIX, Linux), DOS, and Windows.
• Extensive programming skills. Well versed in C, awk, and Perl programming languages.
• Comprehensive experience with molecular mechanics refinements and simulations of macromolecular systems and their complexes.
• Wide array of experience with various molecular modelling packages including Amber, CHARMm, InsightII, RasMol, and Quanta.
• Advanced system administration and internet security skills. Have installed, configured, and maintained all aspects of networked computer systems under Solaris, Irix, Linux, DOS, and Windows platforms, including state-of-the-art cryptography software.
• Broad knowledge of the HTML markup language and related technologies such as JavaScript, CGI programming, SSI, and http servers.
• Experience with GUI programming under the X Window System. Developed and maintain "jaZip," an X Windows-based freeware removable media management application for Linux. "jaZip" is used by thousands of government offices, businesses, and private individuals worldwide, and is endorsed by the software development team at Iomega.
• Extensive knowledge of one- and two-dimensional 1H NMR data collection, processing, and analysis for biological macromolecules.
• Considerable experience in molecular graphics design. Have had graphic art featured on the cover of several publications, including advertisements and promotional items for Nature Structural Biology.

HONORS

• University of California Regents Scholar, 1988-1992.
• UCSB Summer Undergraduate Research Fellowship, 1989-1991.
• UCSB College of Creative Studies Prize Competition scholarship recipient, 1988-1992.
• American Institute of Chemists outstanding Senior Student in Chemistry, 1992.
• Phi Lambda Upsilon National Honorary Chemical Society Award, 1992.
• Willard L. McRary Prize in Chemistry, 1992.

PUBLICATIONS

• Peg S. Eis, Jarrod A. Smith, Jan Rydzewski, David A. Case, Dale L. Boger and Walter J. Chazin. " High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA. " Journal of Molecular Biology 272, 237-252 (1997).
• Jarrod A. Smith, Luigi Gomez-Paloma, David A. Case and Walter J. Chazin. " Molecular dynamics docking driven by NMR derived restraints to determine the structure of calicheamicin g1I oligosaccharide domain complexed to duplex DNA. " Magnetic Resonance in Chemistry 34, S147-S155 (1996).
• Barbara C. M. Potts, Jarrod A. Smith, Mikael Akke, Katsuo Okazaki, Hiroyoshi Hidaka, David A. Case and Walter J. Chazin. " The structure of calcyclin reveals a novel homodimeric fold for S11 Ca2+-binding proteins. " Nature Structural Biology 9, 790-796 (1995).
• Walter J. Chazin, G. Carlström, S.-M. Chen, Siobhan Miick, Luigi Gomez-Paloma, Jarrod A. Smith and Jan Rydzewski. " Complex DNA structures and structures of DNA complexes. " Proceeding of the Symposium on Stable Isotope Applications in Biomolecular Structure & Mechanism, Santa Fe, NM., pp. 43-57 (1995).
• Luigi Gomez-Paloma, Jarrod A. Smith, Walter J. Chazin and K.C. Nicolaou. " The interaction of calicheamicin and DNA: Identification of multiple binding modes and the role of the oligosaccharide domain in binding affinity and sequence selectivity. " Journal of the American Chemical Society 116, 3697-3708 (1994).
• Jarrod A. Smith, Giuseppe Bifulco, Luigi Gomez-Paloma, David A. Case, Dale L. Boger, Walter J. Chazin. " NMR structure of the adduct between (-)-duocarmycin SA and d(GACTAATTGTC)-d(GACAATTAGTC): Implications of structure mediated catalysis. " Manuscript submitted for review.
• Jan Rydzewski, Jarrod A. Smith and Walter J. Chazin. " Three dimensional structure of the DNA minor groove binding agent SN-6999 complexed to an A-tract DNA duplex. " Manuscript ready for submission.
• Jarrod A. Smith, Vickie Tsui, David A. Case. "NMR structure refinements of d(GCGTTAACGC)2: A comparative analysis of methodologies for DNA structure determination. " Manuscript in preparation.

jsmith@scripps.edu