N. M. Agabian, PhD, Professor, Departments of Stomatology, Microbiology and Immunology and Pharmaceutical Chemistry; Chair Graduate Group of Oral Biology 

 D. A. Agard, PhD, Professor, Departments of Biochemistry & Biophysics, and Pharmaceutical Chemistry; Howard Hughes Investigator 

Sauter, N.K., Mau, T., Rader, S.D., and Agard, D.A. (1998). Molecular architecture of a folding catalyst: a-lytic protease complexed with its pro region. Nature Structural Biology 5: 945-950. 

Sohl, J.L., Jaswal, S.S., and Agard, D.A. (1998). Unfolded conformations are more stable than the native state of a-lytic protease. Nature 395: 817-819

P.C. Babbitt, PhD,Associate Professor, Department of Pharmaceutical Chemistry; Head, Bioinformatics Focus Area,  Biological and Medical Informatics Program

Mechanistically diverse enzyme Superfamilies: The Importance of Chemistry in the Evolution of Catalysis. J.A. Gerit and P.C. Babbitt, Cur. Op. Chem. Biol., 2, 607-612 (1998).

New Functions from Old Scaffolds: How NatureRe-engineers Enzymes for New Functions. P. C. Babbitt & John A. Gerlt. in Evolutionary Approaches to Protein Design (series: Advances in Protein Chemistry, Vol. 55.) Edited by Frances H. Arnold, Academic Press, San Diego, CA, (2000) 1-28.

 L. Z. Benet, PhD, Professor, Department of Biopharmaceutical Sciences 

F. M. Brodsky, PhD, Associate Professor, Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and Associate Adjunct Professor, Department of Microbiology and Immunology 

Bursztajn S; Vincent S; Brodsky FM; Benes F; Morris SA.  "A novel AP180-related protein in vesicles that concentrate at acetylcholine receptor clusters." Journal of Cellular Biochemistry, 1998 Mar 15, 68(4):457-71. 

Liu SH; Marks MS; Brodsky FM. "A dominant-negative clathrin mutant differentially affects trafficking of molecules with distinct sorting motifs in the class II major histocompatibility complex (MHC) pathway". Journal of Cell Biology, 1998 Mar 9, 140(5): 1023-37.

 A. L. Burlingame, PhD,Professor, Department of Pharmaceutical Chemistry; Director, NIH/NSF Mass Spectrometry Facility 

F. E. Cohen, MD, PhD, Professor, Department of Cellular and Molecular Pharmacology and Medicine 

Goh, CS; Bogan, AA; Joachimiak, M; Walther, D; Cohen, F.E.  "Co-evolution of proteins with their interaction partners". Journal of Molecular Biology, 2000 Jun 2, 299(2):283-93.

Kaneko, K; Ball, HL; Wille, H; Zhang, H; Groth, D; Torchia, M; Tremblay, P; Safar, J; Prusiner, SB; DeArmond, SJ; Baldwin, MA; Cohen, F.E.  "A synthetic peptide initiates Gerstmann- Sträussler- Scheinker (GSS) disease in transgenic mice". Journal of Molecular Biology, 2000 Jan 28,295(4):997-1007.

 B. R. Conklin, MD, Assistant Professor, Departments of Medicine, and Department of Cellular and Molecular Pharmacology, Gladstone Institute of Cardiovascular Disease 

Redfern, C.H., Degtyarev, M.Y., Kwa, A.T., Salomonis, N., Cotte, N., Nanevicz, T., Fidelman, N., Desai, K., Vranizan, K., Lee, E.K., Coward, P., Shah, N., Warrington, J., Fishman, G.I., Bernstein, D., Baker, A.J., Conklin, B.R.  ,"Conditional expression of a Gi-coupled receptor causes ventricular conduction delay and a lethal cardiomyopathy",  Proc. Natl. Acad. Sci. USA. (2000) 97:48264831.

Redfern, C.H., Coward, P., Degtyarev, M.Y., Lee, E.K., Kwa, A., Hennighausen, L., Bujard, H., Fishman, G.I., Conklin, B.R.  '"Conditional expression and signaling of a specifically designed Gi-coupled receptor in transgenic mice" . Nat. Biotech. (1999) 17:165169.

 C. S. Craik, PhD Professor, Departments of Pharmaceutical Chemistry, Biochemistry & Biophysics, and Cellular & Molecular Pharmacology; Director, Chemistry and Chemical Biology Graduate Group 

Harris JL, Backes BJ, Leonetti F, Mahrus S, Ellman JA, Craik CS. "Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries."  Proc Natl Acad Sci U S A. 2000 97:7754-9.

Takeuchi T, Harris JL, Huang W, Yan KW, Coughlin SR, Craik CS. "Cellular localization of membrane-type serine protease 1 and identification of protease-activated receptor-2 and single-chain urokinase-type plasminogen activator as substrates". J Biol Chem. 2000 275:26333-42.

K. A. Dill, PhD, Professor, Department of Pharmaceutical Chemistry, Biopharmaceutical Sciences, Biochemistry and Biophysics; Adjunct Professor of Pharmaceutics, University of Utah; Research Biophysicist, Lawrence Berkeley Lab 

Dill, K.A.  "Polymer Principles and Protein Folding". Protein Science 8: 1166-1180 (1999).

Dill, K.A. and H.S. Chan.  "From Levinthal to Pathways to Funnels: The "New View" of Protein Folding Kinetics".  Nature Structural Biology 4: 10-19 (1997).

V. Doetsch, PhD, Professor, Departments of Pharmaceutical Chemistry, Cellular and Molecular Pharmacology and Medicine 

T. E. Ferrin, PhD, Professor, Department of Pharmaceutical Chemistry; Director, Computer Graphics Laboratory 

"Integrated Tools for Structural and Sequence Alignment and Analysis". C.C. Huang, W.R. Novak, P.C. Babbitt, A.I. Jewett, T.E. Ferrin, and T.E. Klein, Pacific Symposium on Biocomputing 2000, pp. 230-241. Edited by R.B Altman, A.K Dunker, L. Hunter,  K. Lauderdale, and T.E Klein. World Scientific Publishing, 2000

"MINRMS: An Efficient Algorithm for Determining Protein Structure Similarity Using Root-Mean Squared-Distance."  A.I. Jewett, C.C. Huang, and T.E. Ferrin, Bioinformatics, in-press

 S. J. Fisher, PhD, Professor, Departments of Anatomy, Stomatology, Pharmaceutical Chemistry, Obstetrics, Gynecology and Reproductive Sciences; Associate Director, Mass Spectrometry Facility

Prakobphol, A., Xu, F., Hoang, V.M., Larsson, T., Bergstrom, J., Johansson, I., Frängsmyr, L., Holmskov, U., Leffler, H., Nilsson, C., Borén, T., Wright, J.R., Strömberg, N., and Fisher, S.J.   "Salivary agglutinin, which binds Streptococcus mutansand Helicobacter pylori, is the lung scavenger receptor cysteine-rich protein GP-340".  J. Biol. Chem.  275: 39860-39866, 2000.

Hoang, V.M., Foulk, R., Clauser, K., Burlingame, A., Gibson, B.W., and Fisher, S.J.   "Functional proteomics: examining the effects of hypoxia on the cytotrophoblast protein repertoire". Biochemistry. (in press)

 R. J. Fletterick, PhD, Professor, Departments of Biochemistry & Biophysics, and Cellular and Molecular Pharmacology

Waugh, S.M., Harris, J.L., Fletterick, R.J, and C.S. Craik. (2000)  "The structure of the pro-apoptotic protease granzyme B reveals the molecular determinants of its specificity".  Nature Struct. Biol. 7(9): 762-765.

Wagner, R.L., Shiau, A.K., Huber, B.R., Kelly, A., Scanlan, T.S., Apriletti, J.W., West, B.L., Baxter, J.D., and R.J. Fletterick.  (2000)  "Hormone selectivity in thyroid hormone receptors."  In Press, Molec. Endocrinology.

A. Frankel, PhD, Professor, Departments of Biochemistry & Biophysics, and Cellular and Molecular Pharmacology 

Smith, C. A., Calabro, V., and Frankel, A. D. (2000) "An RNA- binding chameleon".  Molec. Cell 6, 1067-1076.

Campisi, D. M., Calabro, V., and Frankel, A. D. (2001) "Structure- based design of a dimeric RNA-peptide complex", EMBO J. 20, 178-186.

B. W. Gibson, PhD, Adjunct Professor, Department of Pharmaceutical Chemistry, UCSF; Professor and Director of Chemistry, Buck Institute for Age Research, Novato, CA 

J.S. Greenspan, BDS, PhD, Professor and Chairman, Department of Stomatology; Professor, Department of Pathology 

"Oral Mucosal Lesions and HIV Viral Load in the Women's Interagency HIV Study (WIHS)": D. Greenspan, E. Komaroff, M. Redford, J. A. Phelan, M. Navazesh, M. E. A. F. Alves, H. Kamrath, R. Mulligan, C. E. Barr, J. S. Greenspan, JAIDS Journal of Acquired Immune Deficiency Syndrom 25:44-50, 2000

R. K. Guy, Ph.D., Assistant Professor of Pharmaceutical Chemistry, and Cellular & Molecular Pharmacology 

Herradura, P. S.; Pendola, K. A.; Guy, R. K. "Copper-Mediated Cross-Coupling of Aryl Boronic Acids and Alkyl Thiols", Org. Lett. 2000, 2, 2019.

Geistlinger, T. R; Guy, R. K. "An Inhibitor of the Interaction of Thyroid Hormone Receptor b and Glucocorticoid Interacting Protein 1", J. Am. Chem. Soc. 2001, in  press

J.C. Hempel, Ph.D., Associate Director, Molecular Design Institute 

C. A. Hunt, PhD, Associate Professor, Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, the Bioengineering Program, and the Medical Information Science Program 

T. L. James, PhD, Professor, Departments of Pharmaceutical Chemistry & Radiology; Chairman, Department of Pharmaceutical Chemistry

"Determination of the Populations and Structures of Multiple Conformers in an Ensemble from NMR Data: Multiple-Copy Refinement of Nucleic Acid Structures using Floating Weights".  A. Görler, N.B. Ulyanov, and T.L. James. J. Biomolec. NMR, 16, 147-164 (2000).

"Identification of Ligands for RNA Targets via Structure-Based Virtual Screening: HIV-1 TAR." A.V. Filikov, V. Mohan, T.A. Vickers, R.H. Griffey, P.D. Cook, R.A. Abagyan, and T.L. James. J. Comp.-Aided Molecular Design, 14, 593-610 (2000).

S. B. Kahl, PhD, Professor, Department of Pharmaceutical Chemistry

"Toxicology of a Boronated Porphyrin in Dogs".  J. Tibbitts, J.R. Fike, K.R. Lamborn, A.W. Bollen and S.B. Kahl, Photochem. Photobiol. 69, 587-594 (1999)

"Boronated Protoporphyrin (BOPP): Localization in Lysosomes of the Human Glioma Cell Line SF-767 with Uptake Modulated by Lipoprotein Levels".  D.E. Callahan, T.M. Forte, S.M. Javed Afzal, D.F. Deen, S.B. Kahl, K.A. Bjornstad, W.L. Bauer and E.A. Blakely, Int. J. Radiat. Oncol., Biol., and Physics 45, 761-771 (1999).

G. L. Kenyon, PhD, Dean and T.D. Rowe Professor College of Pharmacy, University of Michigan 

M. A. Koda-Kimble, Pharm D, Dean, School of Pharmacy, Professor of Clinical Pharmacy, TJ Long Chair in Chain Pharmacy

P.A. Kollman, PhD, Professor, Department of Pharmaceutical Chemistry 

I. D. Kuntz, PhD, Professor, Departments of Pharmaceutical Chemistry, and Biochemistry and  Biophysics; Director, Molecular Design Institute; Associate Dean of Research, School of Pharmacy

"High Throughput Protein Fold Identification by Using Experimental Constraints Derived from Intramolecular Cross- links and Mass Spectrometry".  M.M. Young, N. Tang, J.C. Hempel, C.M. Oshiro, E. W. Taylor, I.D. Kuntz, B.W. Gibson and G. Dollinger.  Proceedings of the National Academy of Sciences;  Vol. 97, No. 11: 5802-5806 (2000)

"The Maximal Affinity of Ligands". I.D. Kuntz, K. Chen, K.A. Sharp, and P.A. Kollman. Proceedings of the National Academy of Sciences:  Vol. 96:  9997-10002 (1999)

J. H. McKerrow, PhD,MD, Professor, Departments of Pathology, Medicine and Pharmaceutical Chemistry; Director, Tropical Disease Research Unit; Director, Laboratory of Molecular Pathology 

"Cysteine Protease Inhibitors Cure an Experimental Trypanosoma Cruzi Infection". J.C. Engel, P.S. Doyle, I. Hseih and J.H. McKerrow. J.Exp Med., 4, 723-734 (1998). 

"Intracellular Protease Trafficking in Kinetoplastids Is Mediate by the Prodomain". J.A. Huete-Perez, J.C. Engel, J.C. Mottram and J.H. McKerrow. J. Biol. Chem., 274, 16249-16256 (1999).

S. M. Miller, PhD, Associate Professor, Department of Pharmaceutical Chemistry 

(1998) Engst, S. & Miller, S.M. Biochemistry 37, 11496-11507, "Rapid reduction of Hg(II) by mercuric ion reductase does not require the conserved C-terminal cysteine pair using HgBr2 as the substrate".

(1999) Engst, S. & Miller, S.M. Biochemistry 38, 3519-3529, "Alternative routes for entry of HgX2 into the active site of mercuric ion reductase depend on the nature of the X ligands".

N. J. Oppenheimer, PhD, Professor, Department of Pharmaceutical Chemistry 

P. R. Ortiz de Montellano, PhD, Professor, Departments of Pharmaceutical Chemistry

"Crystal Structure of Human Heme Oxygenase-1". D. Schuller, A. Wilks, P.R. Ortiz de Montellano and T. Poulos, Nature Struct. Biol., 6, 860-867 (1999). 

"The AhpC and AhpD Antioxidant Defense System of Mycobacterium tuberculosis". Hillas, P. J., Soto del Alba, F., Oyarzabal, J., Wilks A., and P.R. Ortiz de Montellano, P. R. J. Biol. Chem. 275, 18801-18809 (2000).

W. Sadee, PhD, Professor, Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry; Vice Chair of Academic Affairs and Administration, Department of Biopharmaceutical Sciences 

"Calmodulin binding to G protein-coupling domain of opioid receptors."  D. Wang, W. Sadée, J.M. Quillan.  J. Biol. Chem. 274, 22081-22088(1999).

"Pharmacogenomics: The promise of personalized medicine".  L. Mancinelli, M. Cronin, W. Sadée. AAPS PharmSci  2 (1) article 4 (2000)

T.S. Scanlan, PhD, Assistant Professor, Department of Pharmaceutical Chemistry 

Buchbinder, J.L., Stephenson, R.C., Dresser, M., Pitera, J., Scanlan, T.S. & Fletterick, R.J. (1998). "Biochemical characterization and crystallographic structure of an Escherichia coli protein from the phosphotriesterase gene family". Biochemistry 37, 5096- 5106. 

Fox, T., Scanlan, T.S. & Kollman, P.A. (1997). "Ligand-binding in the catalytic antibody 17E8: a free energy perturbation calculation study". J. Am. Chem. Soc. 119, 11571-11577.

K.M. Shokat, PhD, Associate Professor, Department Cellular and Molecular Pharmacology

Liu, Y., Witucki, L., Shah, K., Bishop, A.C., and Shokat, K.M. (2000) "Src-Abl Tyrosine Kinase Chimeras: Replacement of the Adenine Binding Pocket of c-Abl with v-Src to Swap Nucleotide and Inhibitor Specificities",  Biochemistry 39(47),14400-8

Bishop, A,C., Ubersax, J.A, Petsch, D.C., Matheos, D., Blethrow, J.A., Gray, N.S, Schultz, P.G, Shimizu, E., Tsien, J.Z., Rose, M.D., Wood, J.L., Morgan, D.O., & Kevan M. Shokat.  (2000), "A Molecular Switch for Inhibitor Sensitive Alleles of any Protein Kinase" Nature, 407(6802), 395-401

M. A. Shuman, MD, Professor, Department of Medicine; Associate Director, Program Development, UCSF Comprehensive Cancer Center

Takeuchi T, Shuman M.A., Craik C.S. "Reverse biochemistry: Use of macromolecular protease inhibitors to dissect complex biologic al processes and identify a membrane-type serine protease in epithelial cancer and normal tissue".  Proc. Natl. Acad. Sci. USA. 1999, 96(20):11054-61

Rubenstein, J.L., Kim, J., Ozawa, T., Zhang, M., Westphal, M., Deen, D., and Shuman, M.A.  "Anti-VEGF Treatment of Glioblastoma Prolongs Survival But Results in Increased Vascular Cooption".  Neoplasia. 2000, In Press

R. M. Stroud, MA, PhD, Professor, Departments of Biochemistry & Biophysics, and Pharmaceutical Chemistry 

Schafmeister CE; LaPorte SL; Miercke LJ; Stroud RM. (1997) "A designed four helix bundle protein with native-like structure." Nature Structural Biology, 4(12):1039-46 

Finer-Moore J; Tsutakawa SE; Cherbavaz DR; LaPorte DC; Koshland DE Jr; Stroud RM. (1997) "Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting". Biochemistry, 36(45):13890-6.

F. C. Szoka, PhD, Professor, Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry 

C. C. Wang, PhD, Professor  of Chemistry and Pharmaceutical Chemistry 

Z. Werb, PhD, Professor of Anatomy

 Liu, Z., X. Zhou, S. D. Shapiro, J. M. Shipley, L. A. Dias, R. M. Senior & Z. Werb (2000). "a1-proteinase inhibitor is the critical substrate for gelatinase B/ MMP-9 in vivo". Cell  102: 647-655

Selvarajan, S., L. R. Lund, T. Takeuchi, C. S. Craik & Z. Werb (2001). "A plasminogen cascade dependent on plasma kallikrein is required for adipocyte differentiation".  Nature Cell Biol. 3: 267-275

Associate Faculty of the UCSF Molecular Design Institute

J. M. Blaney, PhD, DuPont Pharmaceutical Research Labs

E.K. Bradley, PhD, DuPont Pharmaceutical Research Labs, Principal Research Scientist

D. Chapman, PhD, Afferent Systems, Inc., President, Founder 

T.J.A. Ewing, PhD, Camitro Corp., Scientist

A.A. Kossiakoff, PhD, Genentech Inc.,Director of Protein Engineering 

E. J. Martin, PhD, Chiron Corp., Senior Scientist, Drug Discovery Research 

D.C. Spellmeyer, PhD, DuPont Pharmaceutical Research Labs

D.C. Roe, PhD,  Sandia National Laboratory, Scientist 

M.J. Ross, PhD, MetaXen LLC,CEO and President

H.J.R. Weintraub, PhD, Genentech Inc., Director of Scientific Computing

J.A. Wells, PhD, Sunesis Pharmaceuticals, CEO 

M.M. Young, PhD,  Sandia National Laboratory, Scientist

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last update 4/9/01