Fellows
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Current | Alumni Leonel Villa Caballero Edgar Gutierrez Toni Jones Vicente M. Reyes Miguel T. Robinson |
Vicente M. Reyes Ph.D. |
Education
B.S., Chemistry (hon.), University of the Philippines, Diliman, Quezon City
B.S., Mathematics (hon.), University of the Philippines, Diliman, Quezon City
Ph.D., California Institute of Technology, Pasadena, CA, USA (mentor, J.N. Abelson)
Postdoctoral, HIV & AIDS Molecular Biology, NIH/NCI Lab. of Tumor Cell Biol.
Postdoctoral, Protein X-ray Crystallography, UCSD Dept. of Chem. & Biochem.
Postdoctoral, Crystallography/Structure-Based Drug Design, TSRI Dept. of Mol. Biol.
Postdoctoral, Structural Bioinformatics/Computational Biology, SDSC & UCSD
Employment
Assistant Project Scientist, Dept. of Pharmacology, UCSD School of Medicine
Research Interests
As a Ph.D. student in the Dept. of Chemistry at Caltech, I studied transfer RNA splicing and processing in S. cerevisiae. Upon graduation, I moved to NCI at NIH to work in the laboratory of R. Gallo on HIV/AIDS molecular and cell biology, focusing on the function of the Rev protein. I did another postdoctoral work at UCSD with Prof. J. Kraut on the catalytic mechanism of the enzyme dihydrofolate reductase using the technique of x-ray crystallography. I then tried to apply my structural biology background to rational drug design at TSRI, working on the potential anti-cancer target enzymes GAR and AICAR transformylases. Finally, in the early 2000’s, approximately when the human genome sequence was completed, I got interested in bioinformatics (specifically structural bioinformatics) and data mining, so I tried to join the PDB group at UCSD’s San Diego Supercomputer Center and started several original projects focusing on structure-based protein function prediction and novel representations of protein 3D structures, which I am developing and refining until now. Thus far, I have developed computational algorithms for the detection of specific ligand binding sites in proteins, protein-protein interactions sites in binary complexes, and for separating the hydrophobic core from the hydrophilic outer layer of proteins, as well as developing a couple of applications of spherical coordinate representation of protein 3D structures.
Publications
Reyes, V.M. “Protein Structures in Spherical Coordinates: Two Applications: a.) Detection of Pockets and Crevices; and b.) Construction of the Hydrophobic Core" (2007e) (to be submitted)
Reyes, V.M. “Two Methods to Quantify Degree of Burial of Ligand Binding Sites in Proteins: The ‘Cutting Plane’ and ‘Tangent Sphere’ Methods” (2007d) (to be submitted)
Reyes, V.M. “A Novel Analytical Method for Structure-Based Prediction of Protein-Protein Interaction Partners.” (2007c) (to be submitted)
Reyes, V.M. “Structure-Based Prediction of Sialic Acid, Retinoic Acid and Heme-bound and Unbound Nitric Oxide Protein Binding Sites.” (2007b) (to be submitted)
Reyes, V.M. “An Exact (Analytical) Algorithm for Structure-Based Protein Function Prediction via Detection of Specific Ligand 3D Binding Site Motifs” (2007a) (submitted & under revision)
Li, W., Byrnes, R.W., Hayes, J., Birnbaum, A., Reyes, V.M., Shahab, A., Mosley, C., Pekurovsky, D., Quinn, G.B., Shindyalov, I.N., Casanova, H., Ang, L., Berman, F., Arzberger, P.W., Miller, M., Bourne, P.E. “The Encyclopedia of Life Project: Grid Software and Deployment.” New Gener. Comp. (2004) 22:127-136.
Bourne, P., Miller, M., Baldridge, K., Baru, C., Berman, F., Byrnes, R., Casanova, H., Cotofana, N., Fountain, T., Greenberg, J., Li, W., Mosley, C., Pekurovsky, D., Quinn, G., Reyes, V., Shin, P., Shindyalov, I., Veretnik, S. “Encyclopedia of Life: to Open New Chapter of Biological Discovery.” SDSC & NPACI EnVision, (2003) Vol. 19, No. 1, pp. 3-5
Reyes, V.M., Greasley, S.E., Stura, E.A., Beardsley, G.P., Wilson, I.A. “Crystallization and preliminary crystallographic investigations of avian 5-aminoimidazole-4-carboxamide ribonucleotide transformylase-inosine monophosphate cyclohydrolase expressed in Escherichia coli.” Acta Crystallogr D Biol Crystallogr. (2000) Aug;56 (Pt 8):1051-4.
Lee, H., *Reyes, V.M., Kraut, J. “Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4.” Biochemistry. (1996) Jun 4;35(22):7012-20. (*corresponding author)
Reyes, V.M., Sawaya, M.R., Brown, K.A., Kraut, J. “Isomorphous crystal structures of Escherichia coli dihydrofolate reductase complexed with folate, 5-deazafolate, and 5,10-dideazatetrahydrofolate: mechanistic implications.” Biochemistry. (1995) Feb 28;34(8):2710-23. Reyes, V.M., Abelson, J.N. “In vitro synthesis of end-mature, intron-containing transfer RNAs.” Methods Enzymol. (1989);180:63-9.
Reyes, V.M., Abelson, J. “Substrate recognition and splice site determination in yeast tRNA splicing.“ Cell. (1988) Nov 18;55(4):719-30.
Reyes, V.M., Abelson, J. “A synthetic substrate for tRNA splicing.” Anal Biochem. 1987 Oct;166(1):90-106.
Reyes, V.M., Newman, A., Abelson, J. “Mutational analysis of the coordinate expression of the yeast tRNA(Arg)-tRNA(Asp) gene tandem.” Mol Cell Biol. (1986) Jul;6(7):2436-42.
Recent Teaching
Bio100 Lectures – HIV/AIDS, Drug Addiction, Diabetes/Obesity (3 lectures)
Biochemistry (SDSU Dept. of Chemistry)
Honors
Bioinformatics Career Development WIA Award, State of California
Postdoctoral Research Fellowship, NIGMS, NIH
John E. Fogarty International Postdoctoral Research Fellowship, NCI, NIH
Contact Information:
Department of Pharmacology 0636
UCSD School of Medicine
9500 Gilman Drive, BSB 3092
La Jolla, CA 92093-0636
Web site: http://pharmacology.ucsd.edu/faculty/reyes.shtml
Email: vreyes@sdsc.edu or vicentemreyes@gmail.com