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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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    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.
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    26. Sullivan DC, Aynechi T, Voelz VA, Kuntz ID. Information content of molecular structures. Biophys J. 2003 Jul; 85(1):174-90. PMID: 12829474.
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    27. Brooijmans N, Kuntz ID. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct. 2003; 32:335-73. PMID: 12574069.
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    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.
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    29. Kuntz ID, Agard DA. Assessment of the role of computations in structural biology. Adv Protein Chem. 2003; 66:1-25. PMID: 14631815.
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    30. Krumrine J, Raubacher F, Brooijmans N, Kuntz I. Principles and methods of docking and ligand design. Methods Biochem Anal. 2003; 44:443-76. PMID: 12647399.
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    31. 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.
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    32. 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.
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    33. Brooijmans N, Sharp KA, Kuntz ID. Stability of macromolecular complexes. Proteins. 2002 Sep 01; 48(4):645-53. PMID: 12211032.
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    34. 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.
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    35. 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.
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    36. Pegg SC, Haresco JJ, Kuntz ID. A genetic algorithm for structure-based de novo design. J Comput Aided Mol Des. 2001 Oct; 15(10):911-33. PMID: 11918076.
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    37. Aronov AM, Munagala NR, Kuntz ID, Wang CC. Virtual screening of combinatorial libraries across a gene family: in search of inhibitors of Giardia lamblia guanine phosphoribosyltransferase. Antimicrob Agents Chemother. 2001 Sep; 45(9):2571-6. PMID: 11502531.
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    38. Harris JL, Niles A, Burdick K, Maffitt M, Backes BJ, Ellman JA, Kuntz I, Haak-Frendscho M, Craik CS. Definition of the extended substrate specificity determinants for beta-tryptases I and II. J Biol Chem. 2001 Sep 14; 276(37):34941-7. PMID: 11438529.
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    39. Ewing TJ, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des. 2001 May; 15(5):411-28. PMID: 11394736.
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    40. Sullivan DC, Kuntz ID. Conformation spaces of proteins. Proteins. 2001 Mar 01; 42(4):495-511. PMID: 11170204.
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    41. Lamb ML, Burdick KW, Toba S, Young MM, Skillman AG, Zou X, Arnold JR, Kuntz ID. Design, docking, and evaluation of multiple libraries against multiple targets. Proteins. 2001 Feb 15; 42(3):296-318. PMID: 11151003.
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    42. Young MM, Tang N, Hempel JC, Oshiro CM, Taylor EW, Kuntz ID, Gibson BW, Dollinger G. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. Proc Natl Acad Sci U S A. 2000 May 23; 97(11):5802-6. PMID: 10811876.
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    43. Aronov AM, Munagala NR, Ortiz De Montellano PR, Kuntz ID, Wang CC. Rational design of selective submicromolar inhibitors of Tritrichomonas foetus hypoxanthine-guanine-xanthine phosphoribosyltransferase. Biochemistry. 2000 Apr 25; 39(16):4684-91. PMID: 10769124.
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    44. Hopkins SC, Vale RD, Kuntz ID. Inhibitors of kinesin activity from structure-based computer screening. Biochemistry. 2000 Mar 14; 39(10):2805-14. PMID: 10704233.
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    45. Makino S, Ewing TJ, Kuntz ID. DREAM++: flexible docking program for virtual combinatorial libraries. J Comput Aided Mol Des. 1999 Sep; 13(5):513-32. PMID: 10483532.
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    46. 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.
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    47. Wang J, Kollman PA, Kuntz ID. Flexible ligand docking: a multistep strategy approach. Proteins. 1999 Jul 01; 36(1):1-19. PMID: 10373002.
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    48. Hendrix DK, Klein TE, Kuntz ID, Klien TE. Macromolecular docking of a three-body system: the recognition of human growth hormone by its receptor. Protein Sci. 1999 May; 8(5):1010-22. PMID: 10338012.
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    49. Young MM, Skillman AG, Kuntz ID. A rapid method for exploring the protein structure universe. Proteins. 1999 Feb 15; 34(3):317-32. PMID: 10024019.
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    50. Stout TJ, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Santi DV, Kuntz ID, Stroud RM, Shoichet BK, Costi MP. Structure-based design of inhibitors specific for bacterial thymidylate synthase. Biochemistry. 1999 Feb 02; 38(5):1607-17. PMID: 9931028.
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    51. Sun Y, Ewing TJ, Skillman AG, Kuntz ID. CombiDOCK: structure-based combinatorial docking and library design. J Comput Aided Mol Des. 1998 Nov; 12(6):597-604. PMID: 9879507.
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    52. Somoza JR, Skillman AG, Munagala NR, Oshiro CM, Knegtel RM, Mpoke S, Fletterick RJ, Kuntz ID, Wang CC. Rational design of novel antimicrobials: blocking purine salvage in a parasitic protozoan. Biochemistry. 1998 Apr 21; 37(16):5344-8. PMID: 9548915.
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    53. Oshiro CM, Kuntz ID. Characterization of receptors with a new negative image: use in molecular docking and lead optimization. Proteins. 1998 Feb 15; 30(3):321-36. PMID: 9517547.
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    54. Hendrix DK, Kuntz ID. Surface solid angle-based site points for molecular docking. Pac Symp Biocomput. 1998; 317-26. PMID: 9697192.
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    55. Selzer PM, Chen X, Chan VJ, Cheng M, Kenyon GL, Kuntz ID, Sakanari JA, Cohen FE, McKerrow JH. Leishmania major: molecular modeling of cysteine proteases and prediction of new nonpeptide inhibitors. Exp Parasitol. 1997 Nov; 87(3):212-21. PMID: 9371086.
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    56. Caldera PS, Yu Z, Knegtel RM, McPhee F, Burlingame AL, Craik CS, Kuntz ID, Ortiz de Montellano PR. Alkylation of a catalytic aspartate group of the SIV protease by an epoxide inhibitor. Bioorg Med Chem. 1997 Nov; 5(11):2019-27. PMID: 9416419.
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    57. Hoffman LR, Kuntz ID, White JM. Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: irreversible inhibition of infectivity. J Virol. 1997 Nov; 71(11):8808-20. PMID: 9343241.
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    58. Chen Q, Shafer RH, Kuntz ID. Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry. 1997 Sep 23; 36(38):11402-7. PMID: 9298959.
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    59. Gschwend DA, Sirawaraporn W, Santi DV, Kuntz ID. Specificity in structure-based drug design: identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase. Proteins. 1997 Sep; 29(1):59-67. PMID: 9294866.
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    60. Knegtel RM, Kuntz ID, Oshiro CM. Molecular docking to ensembles of protein structures. J Mol Biol. 1997 Feb 21; 266(2):424-40. PMID: 9047373.
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    61. McPhee F, Caldera PS, Bemis GW, McDonagh AF, Kuntz ID, Craik CS. Bile pigments as HIV-1 protease inhibitors and their effects on HIV-1 viral maturation and infectivity in vitro. Biochem J. 1996 Dec 01; 320 ( Pt 2):681-6. PMID: 8973584.
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    62. McPhee F, Good AC, Kuntz ID, Craik CS. Engineering human immunodeficiency virus 1 protease heterodimers as macromolecular inhibitors of viral maturation. Proc Natl Acad Sci U S A. 1996 Oct 15; 93(21):11477-81. PMID: 8876160.
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    63. Chen Q, Kuntz ID, Shafer RH. Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye. Proc Natl Acad Sci U S A. 1996 Apr 02; 93(7):2635-9. PMID: 8610093.
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    64. Gschwend DA, Kuntz ID. Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal. J Comput Aided Mol Des. 1996 Apr; 10(2):123-32. PMID: 8741016.
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    65. Gschwend DA, Good AC, Kuntz ID. Molecular docking towards drug discovery. J Mol Recognit. 1996 Mar-Apr; 9(2):175-86. PMID: 8877811.
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    66. Cerpa R, Cohen FE, Kuntz ID. Conformational switching in designed peptides: the helix/sheet transition. Fold Des. 1996; 1(2):91-101. PMID: 9079369.
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    67. Benjamin DR, Markby DW, Bourne HR, Kuntz ID. Solution structure of the GTPase activating domain of alpha s. J Mol Biol. 1995 Dec 08; 254(4):681-91. PMID: 7500342.
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    68. Chapman BS, Kuntz ID. Modeled structure of the 75-kDa neurotrophin receptor. Protein Sci. 1995 Sep; 4(9):1696-707. PMID: 8528068.
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    69. Good AC, Kuntz ID. Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors. J Comput Aided Mol Des. 1995 Aug; 9(4):373-9. PMID: 8523046.
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    70. Roe DC, Kuntz ID. BUILDER v.2: improving the chemistry of a de novo design strategy. J Comput Aided Mol Des. 1995 Jun; 9(3):269-82. PMID: 7561978.
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    71. Oshiro CM, Kuntz ID, Dixon JS. Flexible ligand docking using a genetic algorithm. J Comput Aided Mol Des. 1995 Apr; 9(2):113-30. PMID: 7608743.
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    72. Good AC, Ewing TJ, Gschwend DA, Kuntz ID. New molecular shape descriptors: application in database screening. J Comput Aided Mol Des. 1995 Feb; 9(1):1-12. PMID: 7751866.
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    73. Benjamin DR, Markby DW, Bourne HR, Kuntz ID. Complete 1H, 13C, and 15N assignments and secondary structure of the GTPase activating domain of Gs. Biochemistry. 1995 Jan 10; 34(1):155-62. PMID: 7819191.
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    74. Grootenhuis PD, Roe DC, Kollman PA, Kuntz ID. Finding potential DNA-binding compounds by using molecular shape. J Comput Aided Mol Des. 1994 Dec; 8(6):731-50. PMID: 7738607.
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    75. Meng EC, Kuntz ID, Abraham DJ, Kellogg GE. Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities. J Comput Aided Mol Des. 1994 Jun; 8(3):299-306. PMID: 7964929.
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    76. Aroeti B, Kosen PA, Kuntz ID, Cohen FE, Mostov KE. Mutational and secondary structural analysis of the basolateral sorting signal of the polymeric immunoglobulin receptor. J Cell Biol. 1993 Dec; 123(5):1149-60. PMID: 8245123.
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    77. Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid-body minimization in molecular docking. Proteins. 1993 Nov; 17(3):266-78. PMID: 8272425.
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    78. Shoichet BK, Kuntz ID. Matching chemistry and shape in molecular docking. Protein Eng. 1993 Sep; 6(7):723-32. PMID: 7504257.
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    79. Guiles RD, Basus VJ, Sarma S, Malpure S, Fox KM, Kuntz ID, Waskell L. Novel heteronuclear methods of assignment transfer from a diamagnetic to a paramagnetic protein: application to rat cytochrome b5. Biochemistry. 1993 Aug 17; 32(32):8329-40. PMID: 8347629.
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    80. Rutenber E, Fauman EB, Keenan RJ, Fong S, Furth PS, Ortiz de Montellano PR, Meng E, Kuntz ID, DeCamp DL, Salto R. Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design. J Biol Chem. 1993 Jul 25; 268(21):15343-6. PMID: 8340363.
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    81. Ring CS, Sun E, McKerrow JH, Lee GK, Rosenthal PJ, Kuntz ID, Cohen FE. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc Natl Acad Sci U S A. 1993 Apr 15; 90(8):3583-7. PMID: 8475107.
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    82. Bodian DL, Yamasaki RB, Buswell RL, Stearns JF, White JM, Kuntz ID. Inhibition of the fusion-inducing conformational change of influenza hemagglutinin by benzoquinones and hydroquinones. Biochemistry. 1993 Mar 30; 32(12):2967-78. PMID: 8457561.
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    83. Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM. Structure-based discovery of inhibitors of thymidylate synthase. Science. 1993 Mar 05; 259(5100):1445-50. PMID: 8451640.
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    84. Bemis GW, Kuntz ID. A fast and efficient method for 2D and 3D molecular shape description. J Comput Aided Mol Des. 1992 Dec; 6(6):607-28. PMID: 1291629.
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    85. Guiles RD, Basus VJ, Kuntz ID, Waskell L. Sequence-specific 1H and 15N resonance assignments for both equilibrium forms of the soluble heme binding domain of rat ferrocytochrome b5. Biochemistry. 1992 Nov 24; 31(46):11365-75. PMID: 1332756.
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    86. Kuntz ID. Structure-based strategies for drug design and discovery. Science. 1992 Aug 21; 257(5073):1078-82. PMID: 1509259.
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    87. Kosen PA, Marks CB, Falick AM, Anderson S, Kuntz ID. Disulfide bond-coupled folding of bovine pancreatic trypsin inhibitor derivatives missing one or two disulfide bonds. Biochemistry. 1992 Jun 30; 31(25):5705-17. PMID: 1377024.
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    88. Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID. Automated site-directed drug design using molecular lattices. J Mol Graph. 1992 Jun; 10(2):66-78, 106. PMID: 1637751.
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    89. Hurle MR, Eads CD, Pearlman DA, Seibel GL, Thomason J, Kosen PA, Kollman P, Anderson S, Kuntz ID. Comparison of solution structures of mutant bovine pancreatic trypsin inhibitor proteins using two-dimensional nuclear magnetic resonance. Protein Sci. 1992 Jan; 1(1):91-106. PMID: 1284804.
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    90. Shoichet BK, Kuntz ID. Protein docking and complementarity. J Mol Biol. 1991 Sep 05; 221(1):327-46. PMID: 1920412.
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    91. Daggett V, Kollman PA, Kuntz ID. A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers. 1991 Aug; 31(9):1115-34. PMID: 1786342.
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    92. Altman JD, Henner D, Nilsson B, Anderson S, Kuntz ID. Intracellular expression of BPTI fusion proteins and single column cleavage/affinity purification by chymotrypsin. Protein Eng. 1991 Jun; 4(5):593-600. PMID: 1716367.
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    93. Hurle MR, Anderson S, Kuntz ID. Confirmation of the predicted source of a slow folding reaction: proline 8 of bovine pancreatic trypsin inhibitor. Protein Eng. 1991 Apr; 4(4):451-5. PMID: 1881870.
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    94. Daggett V, Kollman PA, Kuntz ID. Molecular dynamics simulations of small peptides: dependence on dielectric model and pH. Biopolymers. 1991 Feb 15; 31(3):285-304. PMID: 1868159.
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    95. DeCamp DL, Babé LM, Furth P, Ortiz de Montellano P, Kuntz ID, Craik CS. Structure-based inhibition of HIV-1 protease activity and viral infectivity. Adv Exp Med Biol. 1991; 306:489-92. PMID: 1812747.
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    96. Bradley EK, Thomason JF, Cohen FE, Kosen PA, Kuntz ID. Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance. J Mol Biol. 1990 Oct 20; 215(4):607-22. PMID: 2231722.
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    97. Babbitt PC, West BL, Buechter DD, Kuntz ID, Kenyon GL. Removal of a proteolytic activity associated with aggregates formed from expression of creatine kinase in Escherichia coli leads to improved recovery of active enzyme. Biotechnology (N Y). 1990 Oct; 8(10):945-9. PMID: 1370005.
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    98. DesJarlais RL, Seibel GL, Kuntz ID, Furth PS, Alvarez JC, Ortiz de Montellano PR, DeCamp DL, Babé LM, Craik CS. Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. Proc Natl Acad Sci U S A. 1990 Sep; 87(17):6644-8. PMID: 2204060.
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    99. Grootenhuis PD, Kollman PA, Seibel GL, DesJarlais RL, Kuntz ID. Computerized selection of potential DNA binding compounds. Anticancer Drug Des. 1990 Aug; 5(3):237-42. PMID: 2169249.
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    100. Hurle MR, Marks CB, Kosen PA, Anderson S, Kuntz ID. Denaturant-dependent folding of bovine pancreatic trypsin inhibitor mutants with two intact disulfide bonds. Biochemistry. 1990 May 08; 29(18):4410-9. PMID: 1693524.
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    101. Guiles RD, Altman J, Kuntz ID, Waskell L, Lipka JJ. Structural studies of cytochrome b5: complete sequence-specific resonance assignments for the trypsin-solubilized microsomal ferrocytochrome b5 obtained from pig and calf. Biochemistry. 1990 Feb 06; 29(5):1276-89. PMID: 2322562.
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    102. Altman J, Lipka JJ, Kuntz I, Waskell L. Identification by proton nuclear magnetic resonance of the histidines in cytochrome b5 modified by diethyl pyrocarbonate. Biochemistry. 1989 Sep 19; 28(19):7516-23. PMID: 2558710.
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    103. Cohen FE, Gregoret L, Presnell SR, Kuntz ID. Protein structure predictions: new theoretical approaches. Prog Clin Biol Res. 1989; 289:75-85. PMID: 2657754.
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    104. Basus VJ, Billeter M, Love RA, Stroud RM, Kuntz ID. Structural studies of alpha-bungarotoxin. 1. Sequence-specific 1H NMR resonance assignments. Biochemistry. 1988 Apr 19; 27(8):2763-71. PMID: 3401447.
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    105. DesJarlais RL, Sheridan RP, Seibel GL, Dixon JS, Kuntz ID, Venkataraghavan R. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J Med Chem. 1988 Apr; 31(4):722-9. PMID: 3127588.
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    106. 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.
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    107. Kuntz ID. Macromolecular structure in solution. Protein Eng. 1987 Jun; 1(3):147-8. PMID: 3507700.
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    108. Frauenfelder H, Hartmann H, Karplus M, Kuntz ID, Kuriyan J, Parak F, Petsko GA, Ringe D, Tilton RF, Connolly ML. Thermal expansion of a protein. Biochemistry. 1987 Jan 13; 26(1):254-61. PMID: 3828301.
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    109. Cohen FE, Kuntz ID. Prediction of the three-dimensional structure of human growth hormone. Proteins. 1987; 2(2):162-6. PMID: 3447173.
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    110. 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.
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    111. Tilton RF, Kuntz ID, Petsko GA. Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A. Biochemistry. 1984 Jun 19; 23(13):2849-57. PMID: 6466620.
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    112. Tilton RF, Kuntz ID. Nuclear magnetic resonance studies of xenon-129 with myoglobin and hemoglobin. Biochemistry. 1982 Dec 21; 21(26):6850-7. PMID: 7159568.
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    113. Kuntz ID. Structures of proteins. Science. 1980 Oct 24; 210(4468):420. PMID: 17837421.
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    114. Kuntz ID, Kauzmann W. Hydration of proteins and polypeptides. Adv Protein Chem. 1974; 28:239-345. PMID: 4598824.
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    115. Kuntz ID, Brassfield TS. Hydration of macromolecules. II. Effects of urea on protein hydration. Arch Biochem Biophys. 1971 Feb; 142(2):660-4. PMID: 5550166.
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    116. Kuntz ID, Brassfield TS, Law GD, Purcell GV. Hydration of macromolecules. Science. 1969 Mar 21; 163(3873):1329-31. PMID: 5765111.
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    117. Gould ES, Kuntz ID, Calvin M. Absorption changes in bacterial chromatophores. II. A new chlorophyll-like pigment from the oxidation of chromatophores from Rhodospirillum rubrum. Photochem Photobiol. 1965 Jun; 4(3):483-90. PMID: 5873425.
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    118. KUNTZ ID, LOACH PA, CALVIN M. ABSORPTION CHANGES IN BACTERIAL CHROMATOPHORES. Biophys J. 1964 May; 4:227-49. PMID: 14185583.
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    119. RUBY RH, KUNTZ ID, CALVIN M. TRANSIENT EPR AND ABSORBENCE CHANGES IN PHOTPSYNTHETIC BACTERIA. Proc Natl Acad Sci U S A. 1964 Mar; 51:515-20. PMID: 14171949.
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    120. RUBY RH, KUNTZ ID, CALVIN M. A CONTRIBUTION TO THE UNDERSTANDING OF THE PRIMARY QUANTUM CONVERSION IN PHOTOSYNTHESIS. Bull Soc Chim Biol (Paris). 1964; 46:1595-605. PMID: 14270542.
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    121. RUBY RH, KUNTZ ID, CALVIN M. A CONTRIBUTION TO THE UNDERSTANDING OF THE PRIMARY QUANTUM CONVERSION IN PHOTOSYNTHESIS. UCRL-11212. UCRL US At Energy Comm. 1964 Jan; 36:1-19. PMID: 24547359.
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