Irwin D. Kuntz
University of California San Francisco


Princeton University; A.B. 1961 Physical Chemistry
University of California, Berkeley; Ph.D. 1965 Physical Chemistry

1965 - 1971 Assistant Professor, Chemistry, Princeton University
1971 - 1976 Associate Professor, Chemistry and Pharmaceutical Chemistry, UCSF
1972 - 1989  Vice Chairman (Physical Chemistry), Department of Pharmaceutical Chemistry, UCSF
1976 - present Professor, Department of Pharmaceutical Chemistry, UCSF
1987 - 1993 Chairman, Graduate Group in Biophysics, UCSF
1993 - 2002 Director,  Molecular Design Institute, UCSF
1998 - present Associate Dean of Research, School of Pharmacy, UCSF


Phi Beta Kappa;  Sigma Xi; Fellow, AAAS
UCSF Faculty Research Lecturer, 1996


Spectroscopic Recognition of Guanine Dimeric Hairpin Quadruplexes by a Carbocyanine dye.  Q. Chen,  I.D. Kuntz, and R.H. Shafer. Biochem. 93: 2635-2639 (1996)

Conformational Switching in Designed Peptides: the Helix/Sheet Transition.  R. Cerpa, F.E. Cohen, and I.D. Kuntz. Folding  and Design  1:91-101 (1996)

Bile Pigments as HIV-1 Protease Inhibitors and their Effects on HIV-1 Viral MaturationandInfectivity in vitro.  F. McPhee, P.S. Caldera, G. W. Bemis, A. F. McDonagh, I.D. Kuntz, and C. S. Craik.  Biochem. J. Vol 320: 681-686 (1996)

Critical Evaluation of Search Algorithms for Automated Molecular Docking and Database Screening.  T. J. A. Ewing and I.D. Kuntz. J. of Computational Chem. vol 18, no. 9: 1175-1189 (1996)

Structure-Based Design of Parasitic Protease Inhibitors.  R. Li, X. Chen, B. Gong, P.M. Selzer, Z. Li, E. Davidson, G. Kurzban, R. E. Miller, E. O. Nuzum, J. H. McKerrow, R. J. Fletterick, S. A. Gillmor, C.S. Craik, I.D. Kuntz, F.E. Cohen, and G. L. Kenyon.  Bioorganic & Medicinal Chem. vol 4, no. 9, 1421-1427 (1996)

Molecular Docking to Ensembles of Protein Structures.  R.M.A. Knegtel, I.D. Kuntz, and C.M. Oshiro.  J. Mol. Biol. Vol 266, 424-440 (1997)

Structure-Based Design and Combinatorial Chemistry Yield Low Nanomolar Inhibitors of Cathepsin D.  E.K. Kick, D.C. Roe, A.G. Skillman, G. Liu, T.J. Ewing, Y. Sun, I.D. Kuntz, and J. Ellman, JA. Chemistry & Biology. Vol 4, No. 4: 297-307 (1997)

Specificity in Structure-Based Drug Design:  Identification of a Novel, Selective Inhibitor of Pneumocystis carinii  Dihydrofolate Reductase.  D.A. Gschwend, W.  Sirawaraporn, D.V. Santi, and I.D. Kuntz.  Proteins.  Vol. 29, 59-67 (1997)

Structure-Based Identification of an Inducer of the Low-pH Conformational Change in the Influenza Virus Hemagglutinin:  Irreversible Inhibition of Infectivity. L.R. Hoffman, I.D. Kuntz, and J.M. White.  J. Virology.   Vol. 71, No. 11:  8808-8820 (1997)

Automated Flexible Ligand Docking Method and Its Application for Database Search.  S. Makino and I.D. Kuntz.  J. Comp. Chem.  Vol. 18, No. 14:  1812-1825 (1997)

Leishmania major:  Molecular Modeling of Cysteine Proteases and Prediction of New Nonpeptide Inhibitors.  P.M. Selzer, X. Chen, V.J. Chan, M. Cheng, G.L. Kenyon, I.D. Kuntz, J.A. Sakanari, F.E. Cohen, and J.H. McKerrow. Experimental Parasitology.  Vol. 87, 212-221 (1997)

Structure-Based Discovery of Ligands Targeted to the RNA Double Helix. Q. Chen, R.H. Shafer, and I.D. Kuntz.  Biochemistry.  Vol. 36, No. 38:  11402-11407 (1997)

Alkylation of a Catalytic Aspartate Group of the SIV Protease by an Epoxide Inhibitor. P.S. Caldera, Z. Yu, R.M. Knegtel, F. McPhee, A.L. Burlingame, C.S. Craik, I.D. Kuntz, and P.R. Ortiz de Montellano. Bioorganic and Medicinal Chemistry.   Vol. 5, No. 11:  2019-2027 (1997)

Characterization of Receptors With a New Negative Image:  Use in Molecular Docking and Lead Optimization. C.M. Oshiro and I.D. Kuntz.Proteins.  Vol. 30, 321-336 (1998)

Rational Design of Novel Antimicrobials:  Blocking x Salvage in a Parasitic Protozoan. J.R. Somoza, A.G. Skillman, Jr., N.R. Munagala, C.M. Oshiro, R.M. Knegtel, S. Mpoke, R.J.  Fletterick, I.D. Kuntz, and C.C. Wang.  Biochemistry :  Vol. 37, No. 6:  5344-5348 (1998)

ELECT++:  Faster Conformational Search Method for Docking Flexible Molecules Using Molecular Similarity.  S. Makino and I.D. Kuntz.  Journal of Computational Chemistry:  Vol. 19, No. 16:  1834-1852 (1998)

Ligand Solvation in Molecular Docking.  B. K. Shoichet, A.R. Leach, and I.D. Kuntz.  Proteins:  Vol 34, 4-16 (1999)

Macromolecular docking of a three-body system:  The recognition of human growth hormone by its receptor.  D.K. Hendrix, T.E. Klein, and I.D. Kuntz.  Protein Science:  Vol. 8:  1010-1022 (1999)

Potent, Low-Molecular Weight Non-Peptide Inhibitors of Malarial Aspartyl Protease Plasmepsin II.  T.S. Haque, A. G. Skillman, C.E. Lee, H. Habashita, I.Y. Gluzman, T.J.A. Ewing, D.E. Goldberg, I.D. Kuntz, and J.A. Ellman.  Journal of Medicinal Chemistry:  Vol. 42, 1428-1440 (1999)

DREAM++:  Flexible docking program for virtual combinatorial libraries.  S. Makino, T.J.A. Ewing, and I.D. Kuntz.  Journal of Computer-Aided Molecular Design: Vol. 13:  513-532 (1999)

Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model.  X. Zou, Y. Sun, and I.D. Kuntz.  Journal of the American Chemistry Society:  Vol. 121, No. 35:  8033-8043 (1999)

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)

Inhibitors of Kinesin Activity from Structure-Based Computer Screening.  S.C. Hopkins, R.D. Vale, and  I.D. Kuntz.  Biochemistry: Vol. 39, 2805-2814 (2000)

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 Science: Vol. 97, 5802-5806 (2000)

Design, Docking, and Evaluation of Multiple Libraries Against Multiple Targets.  M.L. Lamb, K.W. Burdick, S. Toba, M.M. Young, A.G. Skilllman, X. Zou, J.R. Arnold, and I.D. Kuntz.  Proteins:  Vol. 42:  296-318 (2001)

Conformation Spaces of Proteins.  D.C. Sullivan and I.D. Kuntz.  Proteins, Vol. 42: 495-511 (2001)