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Tack Kuntz, PhD

Title(s)Professor, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Phone415-476-1937
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    Collapse Research 
    Collapse Research Activities and Funding
    Structure Biology and Targeted Drug Design for AIDS
    NIH/NIGMS P01GM056531Sep 1, 1997 - Aug 31, 2007
    Role: Co-Investigator
    Molecular Biophysics Training Grant
    NIH/NIGMS T32GM008284Sep 30, 1988 - Jun 30, 2023
    Role: Principal Investigator
    STRUCTURAL BIOLOGY AND TARGETED DRUG DESIGN FOR AIDS
    NIH/NIGMS P01GM039552Sep 1, 1987 - Aug 31, 1997
    Role: Co-Investigator
    MOLECULAR &CELLULAR BIOPHYSICS STUDY
    NIH U09RG014287Jul 1, 1984 - Jun 30, 1991
    Role: Principal Investigator
    MOLECULAR STRUCTURE IN SOLUTION-A FEASIBILITY STUDY
    NIH R24RR001695Jun 1, 1984 - Nov 30, 1994
    Role: Principal Investigator
    THEORETICAL STUDIES OF MACROMOLECULES
    NIH R01GM031497Mar 1, 1983 - Jun 30, 2003
    Role: Principal Investigator
    MODELING PROTEIN SMALL MOLECULE INTERACTIONS
    NIH R01GM029072Feb 1, 1982 - Jan 31, 2005
    Role: Principal Investigator
    MACROMOLECULAR HYDRATION AND STRUCTURE
    NIH R01GM019267Dec 1, 1977 - Jan 31, 1992
    Role: Principal Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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. PMID: 25914306; PMCID: PMC4469538.
    2. Kuntz ID. Darwinian docking. J Comput Aided Mol Des. 2012 Jan; 26(1):73-5. PMID: 22143893.
      View in: PubMed
    3. 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. PMID: 19369428.
      View in: PubMed
    4. 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. PMID: 18781627.
      View in: PubMed
    5. 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. PMID: 18817429; PMCID: PMC2677910.
    6. 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. PMID: 18201069.
      View in: PubMed
    7. 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. PMID: 17149653.
      View in: PubMed
    8. 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. PMID: 17055267.
      View in: PubMed
    9. 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. PMID: 16677000.
      View in: PubMed
    10. 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. PMID: 26626387.
      View in: PubMed
    11. 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. PMID: 16344478; PMCID: PMC1311738.
    12. Aynechi T, Kuntz ID. An information theoretic approach to macromolecular modeling: II. Force fields. Biophys J. 2005 Nov; 89(5):3008-16. PMID: 16254390; PMCID: PMC1366798.
    13. Aynechi T, Kuntz ID. An information theoretic approach to macromolecular modeling: I. Sequence alignments. Biophys J. 2005 Nov; 89(5):2998-3007. PMID: 16254389; PMCID: PMC1366797.
    14. Lang PT, Kuntz ID, Maggiora GM, Bajorath J. Evaluating the high-throughput screening computations. J Biomol Screen. 2005 Oct; 10(7):649-52. PMID: 16170047.
      View in: PubMed
    15. 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. PMID: 15801834.
      View in: PubMed
    16. 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. PMID: 15506725.
      View in: PubMed
    17. 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. PMID: 15554689.
      View in: PubMed
    18. 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. PMID: 15215090.
      View in: PubMed
    19. 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. PMID: 15214784.
      View in: PubMed
    20. Sullivan DC, Kuntz ID. Distributions in protein conformation space: implications for structure prediction and entropy. Biophys J. 2004 Jul; 87(1):113-20. PMID: 15240450.
      View in: PubMed
    21. 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. PMID: 15163188.
      View in: PubMed
    22. 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. PMID: 14755577.
      View in: PubMed
    23. 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. PMID: 14667217.
      View in: PubMed
    24. 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. PMID: 14518976.
      View in: PubMed
    25. 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. PMID: 12868101.
      View in: PubMed
    26. Sullivan DC, Aynechi T, Voelz VA, Kuntz ID. Information content of molecular structures. Biophys J. 2003 Jul; 85(1):174-90. PMID: 12829474.
      View in: PubMed
    27. Brooijmans N, Kuntz ID. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct. 2003; 32:335-73. PMID: 12574069.
      View in: PubMed
    28. 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. PMID: 12579577.
      View in: PubMed
    29. Kuntz ID, Agard DA. Assessment of the role of computations in structural biology. Adv Protein Chem. 2003; 66:1-25. PMID: 14631815.
      View in: PubMed
    30. 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. PMID: 12642128.
      View in: PubMed
    31. 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. PMID: 12401493.
      View in: PubMed
    32. Brooijmans N, Sharp KA, Kuntz ID. Stability of macromolecular complexes. Proteins. 2002 Sep 01; 48(4):645-53. PMID: 12211032.
      View in: PubMed
    33. 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. PMID: 11959867.
      View in: PubMed
    34. 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. PMID: 11906282.
      View in: PubMed
    35. 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. PMID: 10468550.
      View in: PubMed
    36. 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. PMID: 3351919.
      View in: PubMed
    37. 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. PMID: 3560222.
      View in: PubMed
    38. Kuntz ID, Kauzmann W. Hydration of proteins and polypeptides. Adv Protein Chem. 1974; 28:239-345. PMID: 4598824.
      View in: PubMed