Tack Kuntz, PhD

Professor Emeritus

Department of Pharmaceutical Chemistry

[email protected]

Phone: +1 415 476-1937

Fax: +1 415 502-1655

600 16th St, Rm N472D

UCSF Box 2240

San Francisco, CA 94158

United States

Links

The Kuntz Group

UCSF Profiles

UCSF centers, institutes, and research programs

Founder, UCSF Molecular Design Institute

What I do

Since retiring, I serve as a consultant for current Department faculty.

Degrees

PhD, Physical Chemistry, University of California, Berkeley, 1965

AB, Physical Chemistry, Princeton University, 1961

Research keywords

Molecular Models, Ligands, Nucleic Acids, Macromolecular Substances, proteins

News

Publications

Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. J Comput Chem. 2015 Jun 05; 36(15):1132-56.

Kuntz ID. Darwinian docking. J Comput Aided Mol Des. 2012 Jan; 26(1):73-5.

Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. DOCK 6: combining techniques to model RNA-small molecule complexes. RNA. 2009 Jun; 15(6):1219-30.

Bandyopadhyay P, Kuntz ID. Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction. Biopolymers. 2009 Jan; 91(1):68-77.

Yu ET, Hawkins A, Kuntz ID, Rahn LA, Rothfuss A, Sale K, Young MM, Yang CL, Pancerella CM, Fabris D. The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches. J Proteome Res. 2008 Nov; 7(11):4848-57.

Guo X, Bandyopadhyay P, Schilling B, Young MM, Fujii N, Aynechi T, Guy RK, Kuntz ID, Gibson BW. Partial acetylation of lysine residues improves intraprotein cross-linking. Anal Chem. 2008 Feb 15; 80(4):951-60.

Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC. Development and validation of a modular, extensible docking program: DOCK 5. J Comput Aided Mol Des. 2006 Oct-Nov; 20(10-11):601-19.

Fujii N, Haresco JJ, Novak KA, Gage RM, Pedemonte N, Stokoe D, Kuntz ID, Guy RK. Rational design of a nonpeptide general chemical scaffold for reversible inhibition of PDZ domain interactions. Bioorg Med Chem Lett. 2007 Jan 15; 17(2):549-52.

Lu F, Chi SW, Kim DH, Han KH, Kuntz ID, Guy RK. Proteomimetic libraries: design, synthesis, and evaluation of p53-MDM2 interaction inhibitors. J Comb Chem. 2006 May-Jun; 8(3):315-25.

Rizzo RC, Aynechi T, Case DA, Kuntz ID. Estimation of Absolute Free Energies of Hydration Using Continuum Methods:? Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. J Chem Theory Comput. 2006 Jan; 2(1):128-39.

Ye S, Huang Y, Müllendorff K, Dong L, Giedt G, Meng EC, Cohen FE, Kuntz ID, Weisgraber KH, Mahley RW. Apolipoprotein (apo) E4 enhances amyloid beta peptide production in cultured neuronal cells: apoE structure as a potential therapeutic target. Proc Natl Acad Sci U S A. 2005 Dec 20; 102(51):18700-5.

Aynechi T, Kuntz ID. An information theoretic approach to macromolecular modeling: I. Sequence alignments. Biophys J. 2005 Nov; 89(5):2998-3007.

Aynechi T, Kuntz ID. An information theoretic approach to macromolecular modeling: II. Force fields. Biophys J. 2005 Nov; 89(5):3008-16.

Lang PT, Kuntz ID, Maggiora GM, Bajorath J. Evaluating the high-throughput screening computations. J Biomol Screen. 2005 Oct; 10(7):649-52.

Wang J, Kang X, Kuntz ID, Kollman PA. Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. J Med Chem. 2005 Apr 07; 48(7):2432-44.

Chambers JJ, Gouda H, Young DM, Kuntz ID, England PM. Photochemically knocking out glutamate receptors in vivo. J Am Chem Soc. 2004 Nov 03; 126(43):13886-7.

Arnold JR, Burdick KW, Pegg SC, Toba S, Lamb ML, Kuntz ID. SitePrint: three-dimensional pharmacophore descriptors derived from protein binding sites for family based active site analysis, classification, and drug design. J Chem Inf Comput Sci. 2004 Nov-Dec; 44(6):2190-8.

Verras A, Kuntz ID, Ortiz de Montellano PR. Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes. J Med Chem. 2004 Jul 01; 47(14):3572-9.

Sullivan DC, Kuntz ID. Distributions in protein conformation space: implications for structure prediction and entropy. Biophys J. 2004 Jul; 87(1):113-20.

Koshkin A, Zhou XT, Kraus CN, Brenner JM, Bandyopadhyay P, Kuntz ID, Barry CE, Ortiz de Montellano PR. Inhibition of Mycobacterium tuberculosis AhpD, an element of the peroxiredoxin defense against oxidative stress. Antimicrob Agents Chemother. 2004 Jul; 48(7):2424-30.

Rizzo RC, Toba S, Kuntz ID. A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations. J Med Chem. 2004 Jun 03; 47(12):3065-74.

Kang X, Shafer RH, Kuntz ID. Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK. Biopolymers. 2004 Feb 05; 73(2):192-204.

Masukawa KM, Kollman PA, Kuntz ID. Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. J Med Chem. 2003 Dec 18; 46(26):5628-37.

Fujii N, Haresco JJ, Novak KA, Stokoe D, Kuntz ID, Guy RK. A selective irreversible inhibitor targeting a PDZ protein interaction domain. J Am Chem Soc. 2003 Oct 08; 125(40):12074-5.

Chong LT, Bandyopadhyay P, Scanlan TS, Kuntz ID, Kollman PA. Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. J Comput Chem. 2003 Sep; 24(12):1371-7.

Sullivan DC, Aynechi T, Voelz VA, Kuntz ID. Information content of molecular structures. Biophys J. 2003 Jul; 85(1):174-90.

Brooijmans N, Kuntz ID. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct. 2003; 32:335-73.

Kuntz ID, Agard DA. Assessment of the role of computations in structural biology. Adv Protein Chem. 2003; 66:1-25.

Gouda H, Kuntz ID, Case DA, Kollman PA. Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopolymers. 2003 Jan; 68(1):16-34.

Skillman AG, Maurer KW, Roe DC, Stauber MJ, Eargle D, Ewing TJ, Muscate A, Davioud-Charvet E, Medaglia MV, Fisher RJ, Arnold E, Gao HQ, Buckheit R, Boyer PL, Hughes SH, Kuntz ID, Kenyon GL. A novel mechanism for inhibition of HIV-1 reverse transcriptase. Bioorg Chem. 2002 Dec; 30(6):443-58.

Greenbaum DC, Arnold WD, Lu F, Hayrapetian L, Baruch A, Krumrine J, Toba S, Chehade K, Brömme D, Kuntz ID, Bogyo M. Small molecule affinity fingerprinting. A tool for enzyme family subclassification, target identification, and inhibitor design. Chem Biol. 2002 Oct; 9(10):1085-94.

Brooijmans N, Sharp KA, Kuntz ID. Stability of macromolecular complexes. Proteins. 2002 Sep 01; 48(4):645-53.

Laboissière MC, Young MM, Pinho RG, Todd S, Fletterick RJ, Kuntz I, Craik CS. Computer-assisted mutagenesis of ecotin to engineer its secondary binding site for urokinase inhibition. J Biol Chem. 2002 Jul 19; 277(29):26623-31.

Huo S, Wang J, Cieplak P, Kollman PA, Kuntz ID. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J Med Chem. 2002 Mar 28; 45(7):1412-9.

Kuntz ID, Chen K, Sharp KA, Kollman PA. The maximal affinity of ligands. Proc Natl Acad Sci U S A. 1999 Aug 31; 96(18):9997-10002.

Tilton RF, Singh UC, Kuntz ID, Kollman PA. Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex. J Mol Biol. 1988 Jan 05; 199(1):195-211.

Tilton RF, Singh UC, Weiner SJ, Connolly ML, Kuntz ID, Kollman PA, Max N, Case DA. Computational studies of the interaction of myoglobin and xenon. J Mol Biol. 1986 Nov 20; 192(2):443-56.

Kuntz ID, Kauzmann W. Hydration of proteins and polypeptides. Adv Protein Chem. 1974; 28:239-345.

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