Tack Kuntz, PhD
Professor
Pharmaceutical Chemistry
School of Pharmacy

Websites

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• Profile at mdi.ucsf.edu (mdi.ucsf.edu)

Grants and Projects

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• Molecular Biophysics Training Grant, NIH, 1988-2023
• Resource for Biocomputing, Visualization, and Informatics, NIH/NCRR, 1976-2012
• Structure Biology and Targeted Drug Design for AIDS, NIH, 1997-2007
• Modeling Protein Small Molecule Interactions, NIH, 1982-2005
• Theoretical Studies of Macromolecules, NIH, 1983-2003
• Structural Biology and Targeted Drug Design for Aids, NIH, 1987-1997
• Molecular Structure in Solution-a Feasibility Study, NIH, 1984-1994
• Macromolecular Hydration and Structure, NIH, 1977-1992
• Molecular &Cellular Biophysics Study, NIH, 1984-1991

Publications (112)

Top publication keywords:
Computer SimulationAprotininThermodynamicsNucleic AcidsProtein ConformationProteinsTetrahydrofolate DehydrogenaseModels, ChemicalLigandsModels, MolecularBinding SitesSoftwareAlgorithmsDrug DesignProtein Folding

• DOCK 6: Impact of new features and current docking performance.
  Journal of computational chemistry 2015 Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC
• Darwinian docking.
  Journal of computer-aided molecular design 2011 Kuntz ID
• DOCK 6: combining techniques to model RNA-small molecule complexes.
  RNA (New York, N.Y.) 2009 Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID
• Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction.
  Biopolymers 2009 Bandyopadhyay P, Kuntz ID
• The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches.
  Journal of proteome research 2008 Yu ET, Hawkins A, Kuntz ID, Rahn LA, Rothfuss A, Sale K, Young MM, Yang CL, Pancerella CM, Fabris D

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• Partial acetylation of lysine residues improves intraprotein cross-linking.
  Analytical chemistry 2008 Guo X, Bandyopadhyay P, Schilling B, Young MM, Fujii N, Aynechi T, Guy RK, Kuntz ID, Gibson BW
• Development and validation of a modular, extensible docking program: DOCK 5.
  Journal of computer-aided molecular design 2006 Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC
• Rational design of a nonpeptide general chemical scaffold for reversible inhibition of PDZ domain interactions.
  Bioorganic & medicinal chemistry letters 2006 Fujii N, Haresco JJ, Novak KA, Gage RM, Pedemonte N, Stokoe D, Kuntz ID, Guy RK
• Proteomimetic libraries: design, synthesis, and evaluation of p53-MDM2 interaction inhibitors.
  Journal of combinatorial chemistry 2006 Lu F, Chi SW, Kim DH, Han KH, Kuntz ID, Guy RK
• Estimation of Absolute Free Energies of Hydration Using Continuum Methods:  Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions.
  Journal of chemical theory and computation 2006 Rizzo RC, Aynechi T, Case DA, Kuntz ID
• Apolipoprotein (apo) E4 enhances amyloid beta peptide production in cultured neuronal cells: apoE structure as a potential therapeutic target.
  Proceedings of the National Academy of Sciences of the United States of America 2005 Ye S, Huang Y, Müllendorff K, Dong L, Giedt G, Meng EC, Cohen FE, Kuntz ID, Weisgraber KH, Mahley RW
• An information theoretic approach to macromolecular modeling: I. Sequence alignments.
  Biophysical journal 2005 Aynechi T, Kuntz ID
• An information theoretic approach to macromolecular modeling: II. Force fields.
  Biophysical journal 2005 Aynechi T, Kuntz ID
• Evaluating the high-throughput screening computations.
  Journal of biomolecular screening 2005 Lang PT, Kuntz ID, Maggiora GM, Bajorath J
• Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA.
  Journal of medicinal chemistry 2005 Wang J, Kang X, Kuntz ID, Kollman PA
• Photochemically knocking out glutamate receptors in vivo.
  Journal of the American Chemical Society 2004 Chambers JJ, Gouda H, Young DM, Kuntz ID, England PM
• SitePrint: three-dimensional pharmacophore descriptors derived from protein binding sites for family based active site analysis, classification, and drug design.
  Journal of chemical information and computer sciences 2004 Arnold JR, Burdick KW, Pegg SC, Toba S, Lamb ML, Kuntz ID
• Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes.
  Journal of medicinal chemistry 2004 Verras A, Kuntz ID, Ortiz de Montellano PR
• Distributions in protein conformation space: implications for structure prediction and entropy.
  Biophysical journal 2004 Sullivan DC, Kuntz ID
• Inhibition of Mycobacterium tuberculosis AhpD, an element of the peroxiredoxin defense against oxidative stress.
  Antimicrobial agents and chemotherapy 2004 Koshkin A, Zhou XT, Kraus CN, Brenner JM, Bandyopadhyay P, Kuntz ID, Barry CE, Ortiz de Montellano PR
• A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations.
  Journal of medicinal chemistry 2004 Rizzo RC, Toba S, Kuntz ID
• Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK.
  Biopolymers 2004 Kang X, Shafer RH, Kuntz ID
• Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations.
  Journal of medicinal chemistry 2003 Masukawa KM, Kollman PA, Kuntz ID
• A selective irreversible inhibitor targeting a PDZ protein interaction domain.
  Journal of the American Chemical Society 2003 Fujii N, Haresco JJ, Novak KA, Stokoe D, Kuntz ID, Guy RK
• Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9.
  Journal of computational chemistry 2003 Chong LT, Bandyopadhyay P, Scanlan TS, Kuntz ID, Kollman PA
• Information content of molecular structures.
  Biophysical journal 2003 Sullivan DC, Aynechi T, Voelz VA, Kuntz ID
• Molecular recognition and docking algorithms.
  Annual review of biophysics and biomolecular structure 2003 Brooijmans N, Kuntz ID
• Assessment of the role of computations in structural biology.
  Advances in protein chemistry 2003 Kuntz ID, Agard DA
• Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods.
  Biopolymers 2003 Gouda H, Kuntz ID, Case DA, Kollman PA
• Principles and methods of docking and ligand design.
  Methods of biochemical analysis 2003 Krumrine J, Raubacher F, Brooijmans N, Kuntz I
• A novel mechanism for inhibition of HIV-1 reverse transcriptase.
  Bioorganic chemistry 2002 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
• Stability of macromolecular complexes.
  Proteins 2002 Brooijmans N, Sharp KA, Kuntz ID
• Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design.
  Journal of medicinal chemistry 2002 Huo S, Wang J, Cieplak P, Kollman PA, Kuntz ID
• A genetic algorithm for structure-based de novo design.
  Journal of computer-aided molecular design 2001 Pegg SC, Haresco JJ, Kuntz ID
• Definition of the extended substrate specificity determinants for beta-tryptases I and II.
  The Journal of biological chemistry 2001 Harris JL, Niles A, Burdick K, Maffitt M, Backes BJ, Ellman JA, Kuntz I, Haak-Frendscho M, Craik CS
• Conformation spaces of proteins.
  Proteins 2001 Sullivan DC, Kuntz ID
• Design, docking, and evaluation of multiple libraries against multiple targets.
  Proteins 2001 Lamb ML, Burdick KW, Toba S, Young MM, Skillman AG, Zou X, Arnold JR, Kuntz ID
• High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.
  Proceedings of the National Academy of Sciences of the United States of America 2000 Young MM, Tang N, Hempel JC, Oshiro CM, Taylor EW, Kuntz ID, Gibson BW, Dollinger G
• Rational design of selective submicromolar inhibitors of Tritrichomonas foetus hypoxanthine-guanine-xanthine phosphoribosyltransferase.
  Biochemistry 2000 Aronov AM, Munagala NR, Ortiz De Montellano PR, Kuntz ID, Wang CC
• Inhibitors of kinesin activity from structure-based computer screening.
  Biochemistry 2000 Hopkins SC, Vale RD, Kuntz ID
• DREAM++: flexible docking program for virtual combinatorial libraries.
  Journal of computer-aided molecular design 1999 Makino S, Ewing TJ, Kuntz ID
• The maximal affinity of ligands.
  Proceedings of the National Academy of Sciences of the United States of America 1999 Kuntz ID, Chen K, Sharp KA, Kollman PA
• Flexible ligand docking: a multistep strategy approach.
  Proteins 1999 Wang J, Kollman PA, Kuntz ID
• Macromolecular docking of a three-body system: the recognition of human growth hormone by its receptor.
  Protein science : a publication of the Protein Society 1999 Hendrix DK, Klein TE, Kuntz ID, Klien TE
• A rapid method for exploring the protein structure universe.
  Proteins 1999 Young MM, Skillman AG, Kuntz ID
• Structure-based design of inhibitors specific for bacterial thymidylate synthase.
  Biochemistry 1999 Stout TJ, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Santi DV, Kuntz ID, Stroud RM, Shoichet BK, Costi MP
• CombiDOCK: structure-based combinatorial docking and library design.
  Journal of computer-aided molecular design 1998 Sun Y, Ewing TJ, Skillman AG, Kuntz ID
• Rational design of novel antimicrobials: blocking purine salvage in a parasitic protozoan.
  Biochemistry 1998 Somoza JR, Skillman AG, Munagala NR, Oshiro CM, Knegtel RM, Mpoke S, Fletterick RJ, Kuntz ID, Wang CC
• Characterization of receptors with a new negative image: use in molecular docking and lead optimization.
  Proteins 1998 Oshiro CM, Kuntz ID
• Surface solid angle-based site points for molecular docking.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1998 Hendrix DK, Kuntz ID
• Alkylation of a catalytic aspartate group of the SIV protease by an epoxide inhibitor.
  Bioorganic & medicinal chemistry 1997 Caldera PS, Yu Z, Knegtel RM, McPhee F, Burlingame AL, Craik CS, Kuntz ID, Ortiz de Montellano PR
• Leishmania major: molecular modeling of cysteine proteases and prediction of new nonpeptide inhibitors.
  Experimental parasitology 1997 Selzer PM, Chen X, Chan VJ, Cheng M, Kenyon GL, Kuntz ID, Sakanari JA, Cohen FE, McKerrow JH
• Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: irreversible inhibition of infectivity.
  Journal of virology 1997 Hoffman LR, Kuntz ID, White JM
• Structure-based discovery of ligands targeted to the RNA double helix.
  Biochemistry 1997 Chen Q, Shafer RH, Kuntz ID
• Specificity in structure-based drug design: identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase.
  Proteins 1997 Gschwend DA, Sirawaraporn W, Santi DV, Kuntz ID
• Molecular docking to ensembles of protein structures.
  Journal of molecular biology 1997 Knegtel RM, Kuntz ID, Oshiro CM
• Bile pigments as HIV-1 protease inhibitors and their effects on HIV-1 viral maturation and infectivity in vitro.
  The Biochemical journal 1996 McPhee F, Caldera PS, Bemis GW, McDonagh AF, Kuntz ID, Craik CS
• Engineering human immunodeficiency virus 1 protease heterodimers as macromolecular inhibitors of viral maturation.
  Proceedings of the National Academy of Sciences of the United States of America 1996 McPhee F, Good AC, Kuntz ID, Craik CS
• Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye.
  Proceedings of the National Academy of Sciences of the United States of America 1996 Chen Q, Kuntz ID, Shafer RH
• Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal.
  Journal of computer-aided molecular design 1996 Gschwend DA, Kuntz ID
• Molecular docking towards drug discovery.
  Journal of molecular recognition : JMR 1996 Gschwend DA, Good AC, Kuntz ID
• Conformational switching in designed peptides: the helix/sheet transition.
  Folding & design 1996 Cerpa R, Cohen FE, Kuntz ID
• Solution structure of the GTPase activating domain of alpha s.
  Journal of molecular biology 1995 Benjamin DR, Markby DW, Bourne HR, Kuntz ID
• Modeled structure of the 75-kDa neurotrophin receptor.
  Protein science : a publication of the Protein Society 1995 Chapman BS, Kuntz ID
• Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors.
  Journal of computer-aided molecular design 1995 Good AC, Kuntz ID
• BUILDER v.2: improving the chemistry of a de novo design strategy.
  Journal of computer-aided molecular design 1995 Roe DC, Kuntz ID
• Flexible ligand docking using a genetic algorithm.
  Journal of computer-aided molecular design 1995 Oshiro CM, Kuntz ID, Dixon JS
• New molecular shape descriptors: application in database screening.
  Journal of computer-aided molecular design 1995 Good AC, Ewing TJ, Gschwend DA, Kuntz ID
• Complete 1H, 13C, and 15N assignments and secondary structure of the GTPase activating domain of Gs.
  Biochemistry 1995 Benjamin DR, Markby DW, Bourne HR, Kuntz ID
• Finding potential DNA-binding compounds by using molecular shape.
  Journal of computer-aided molecular design 1994 Grootenhuis PD, Roe DC, Kollman PA, Kuntz ID
• Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities.
  Journal of computer-aided molecular design 1994 Meng EC, Kuntz ID, Abraham DJ, Kellogg GE
• Mutational and secondary structural analysis of the basolateral sorting signal of the polymeric immunoglobulin receptor.
  The Journal of cell biology 1993 Aroeti B, Kosen PA, Kuntz ID, Cohen FE, Mostov KE
• Orientational sampling and rigid-body minimization in molecular docking.
  Proteins 1993 Meng EC, Gschwend DA, Blaney JM, Kuntz ID
• Matching chemistry and shape in molecular docking.
  Protein engineering 1993 Shoichet BK, Kuntz ID
• Novel heteronuclear methods of assignment transfer from a diamagnetic to a paramagnetic protein: application to rat cytochrome b5.
  Biochemistry 1993 Guiles RD, Basus VJ, Sarma S, Malpure S, Fox KM, Kuntz ID, Waskell L
• Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design.
  The Journal of biological chemistry 1993 Rutenber E, Fauman EB, Keenan RJ, Fong S, Furth PS, Ortiz de Montellano PR, Meng E, Kuntz ID, DeCamp DL, Salto R
• Structure-based inhibitor design by using protein models for the development of antiparasitic agents.
  Proceedings of the National Academy of Sciences of the United States of America 1993 Ring CS, Sun E, McKerrow JH, Lee GK, Rosenthal PJ, Kuntz ID, Cohen FE
• Inhibition of the fusion-inducing conformational change of influenza hemagglutinin by benzoquinones and hydroquinones.
  Biochemistry 1993 Bodian DL, Yamasaki RB, Buswell RL, Stearns JF, White JM, Kuntz ID
• Structure-based discovery of inhibitors of thymidylate synthase.
  Science (New York, N.Y.) 1993 Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM
• A fast and efficient method for 2D and 3D molecular shape description.
  Journal of computer-aided molecular design 1992 Bemis GW, Kuntz ID
• Sequence-specific 1H and 15N resonance assignments for both equilibrium forms of the soluble heme binding domain of rat ferrocytochrome b5.
  Biochemistry 1992 Guiles RD, Basus VJ, Kuntz ID, Waskell L
• Structure-based strategies for drug design and discovery.
  Science (New York, N.Y.) 1992 Kuntz ID
• Disulfide bond-coupled folding of bovine pancreatic trypsin inhibitor derivatives missing one or two disulfide bonds.
  Biochemistry 1992 Kosen PA, Marks CB, Falick AM, Anderson S, Kuntz ID
• Automated site-directed drug design using molecular lattices.
  Journal of molecular graphics 1992 Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID
• Comparison of solution structures of mutant bovine pancreatic trypsin inhibitor proteins using two-dimensional nuclear magnetic resonance.
  Protein science : a publication of the Protein Society 1992 Hurle MR, Eads CD, Pearlman DA, Seibel GL, Thomason J, Kosen PA, Kollman P, Anderson S, Kuntz ID
• Protein docking and complementarity.
  Journal of molecular biology 1991 Shoichet BK, Kuntz ID
• A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions.
  Biopolymers 1991 Daggett V, Kollman PA, Kuntz ID
• Intracellular expression of BPTI fusion proteins and single column cleavage/affinity purification by chymotrypsin.
  Protein engineering 1991 Altman JD, Henner D, Nilsson B, Anderson S, Kuntz ID
• Confirmation of the predicted source of a slow folding reaction: proline 8 of bovine pancreatic trypsin inhibitor.
  Protein engineering 1991 Hurle MR, Anderson S, Kuntz ID
• Molecular dynamics simulations of small peptides: dependence on dielectric model and pH.
  Biopolymers 1991 Daggett V, Kollman PA, Kuntz ID
• Structure-based inhibition of HIV-1 protease activity and viral infectivity.
  Advances in experimental medicine and biology 1991 DeCamp DL, Babé LM, Furth P, Ortiz de Montellano P, Kuntz ID, Craik CS
• Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance.
  Journal of molecular biology 1990 Bradley EK, Thomason JF, Cohen FE, Kosen PA, Kuntz ID
• Removal of a proteolytic activity associated with aggregates formed from expression of creatine kinase in Escherichia coli leads to improved recovery of active enzyme.
  Bio/technology (Nature Publishing Company) 1990 Babbitt PC, West BL, Buechter DD, Kuntz ID, Kenyon GL
• Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease.
  Proceedings of the National Academy of Sciences of the United States of America 1990 DesJarlais RL, Seibel GL, Kuntz ID, Furth PS, Alvarez JC, Ortiz de Montellano PR, DeCamp DL, Babé LM, Craik CS
• Computerized selection of potential DNA binding compounds.
  Anti-cancer drug design 1990 Grootenhuis PD, Kollman PA, Seibel GL, DesJarlais RL, Kuntz ID
• Denaturant-dependent folding of bovine pancreatic trypsin inhibitor mutants with two intact disulfide bonds.
  Biochemistry 1990 Hurle MR, Marks CB, Kosen PA, Anderson S, Kuntz ID
• Structural studies of cytochrome b5: complete sequence-specific resonance assignments for the trypsin-solubilized microsomal ferrocytochrome b5 obtained from pig and calf.
  Biochemistry 1990 Guiles RD, Altman J, Kuntz ID, Waskell L, Lipka JJ
• Identification by proton nuclear magnetic resonance of the histidines in cytochrome b5 modified by diethyl pyrocarbonate.
  Biochemistry 1989 Altman J, Lipka JJ, Kuntz I, Waskell L
• Protein structure predictions: new theoretical approaches.
  Progress in clinical and biological research 1989 Cohen FE, Gregoret L, Presnell SR, Kuntz ID
• Structural studies of alpha-bungarotoxin. 1. Sequence-specific 1H NMR resonance assignments.
  Biochemistry 1988 Basus VJ, Billeter M, Love RA, Stroud RM, Kuntz ID
• Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.
  Journal of medicinal chemistry 1988 DesJarlais RL, Sheridan RP, Seibel GL, Dixon JS, Kuntz ID, Venkataraghavan R
• Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex.
  Journal of molecular biology 1988 Tilton RF, Singh UC, Kuntz ID, Kollman PA
• Macromolecular structure in solution.
  Protein engineering 1987 Kuntz ID
• Thermal expansion of a protein.
  Biochemistry 1987 Frauenfelder H, Hartmann H, Karplus M, Kuntz ID, Kuriyan J, Parak F, Petsko GA, Ringe D, Tilton RF, Connolly ML
• Prediction of the three-dimensional structure of human growth hormone.
  Proteins 1987 Cohen FE, Kuntz ID
• Computational studies of the interaction of myoglobin and xenon.
  Journal of molecular biology 1986 Tilton RF, Singh UC, Weiner SJ, Connolly ML, Kuntz ID, Kollman PA, Max N, Case DA
• Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A.
  Biochemistry 1984 Tilton RF, Kuntz ID, Petsko GA
• Nuclear magnetic resonance studies of xenon-129 with myoglobin and hemoglobin.
  Biochemistry 1982 Tilton RF, Kuntz ID
• Hydration of proteins and polypeptides.
  Advances in protein chemistry 1974 Kuntz ID, Kauzmann W
• Hydration of macromolecules. II. Effects of urea on protein hydration.
  Archives of biochemistry and biophysics 1971 Kuntz ID, Brassfield TS
• Hydration of macromolecules.
  Science (New York, N.Y.) 1969 Kuntz ID, Brassfield TS, Law GD, Purcell GV
• ABSORPTION CHANGES IN BACTERIAL CHROMATOPHORES.
  Biophysical journal 1964 KUNTZ ID, LOACH PA, CALVIN M