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Irwin D. Tack Kuntz, Ph.D. - Publications

Affiliations: 
1965-1971 Chemistry Princeton University, Princeton, NJ 
 1971-2003 Pharmaceutical Chemistry University of California, San Francisco, San Francisco, CA 
Area:
determination of protein structure in solution, fast folding processes in proteins, and structure based molecular design
Website:
http://dock.compbio.ucsf.edu/Group/group.html
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Year Citation  Score
2015 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. Journal of Computational Chemistry. 36: 1132-56. PMID 25914306 DOI: 10.1002/Jcc.23905  0.747
2009 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 (New York, N.Y.). 15: 1219-30. PMID 19369428 DOI: 10.1261/Rna.1563609  0.661
2009 Bandyopadhyay P, Kuntz ID. Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction. Biopolymers. 91: 68-77. PMID 18781627 DOI: 10.1002/Bip.21083  0.543
2008 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. Analytical Chemistry. 80: 951-60. PMID 18201069 DOI: 10.1021/Ac701636W  0.748
2007 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. Bioorganic & Medicinal Chemistry Letters. 17: 549-52. PMID 17055267 DOI: 10.1016/J.Bmcl.2006.10.006  0.47
2006 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. Journal of Chemical Theory and Computation. 2: 128-39. PMID 26626387 DOI: 10.1021/Ct050097L  0.771
2006 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. Journal of Computer-Aided Molecular Design. 20: 601-19. PMID 17149653 DOI: 10.1007/S10822-006-9060-4  0.7
2006 Lu F, Chi SW, Kim DH, Han KH, Kuntz ID, Guy RK. Proteomimetic libraries: design, synthesis, and evaluation of p53-MDM2 interaction inhibitors. Journal of Combinatorial Chemistry. 8: 315-25. PMID 16677000 DOI: 10.1021/cc050142v  0.574
2006 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 Journal of Chemical Theory and Computation. 2: 128-139. DOI: 10.1021/ct050097l  0.75
2006 Therese Lang P, Aynechi T, Moustakas D, Shoichet B, Kuntz ID, Brooijmans N, Oshiro CM. Molecular Docking and Structure-Based Design Drug Discovery Research: New Frontiers in the Post-Genomic Era. 1-23. DOI: 10.1002/9780470131862.ch1  0.745
2005 Aynechi T, Kuntz ID. An information theoretic approach to macromolecular modeling: II. Force fields. Biophysical Journal. 89: 3008-16. PMID 16254390 DOI: 10.1529/Biophysj.105.059618  0.766
2005 Aynechi T, Kuntz ID. An information theoretic approach to macromolecular modeling: I. Sequence alignments. Biophysical Journal. 89: 2998-3007. PMID 16254389 DOI: 10.1529/Biophysj.104.054072  0.758
2005 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. Journal of Medicinal Chemistry. 48: 2432-44. PMID 15801834 DOI: 10.1021/Jm049606E  0.424
2004 Sullivan DC, Kuntz ID. Distributions in protein conformation space: implications for structure prediction and entropy. Biophysical Journal. 87: 113-20. PMID 15240450 DOI: 10.1529/Biophysj.104.041723  0.507
2004 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. Antimicrobial Agents and Chemotherapy. 48: 2424-30. PMID 15215090 DOI: 10.1128/Aac.48.7.2424-2430.2004  0.486
2003 Masukawa KM, Kollman PA, Kuntz ID. Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. Journal of Medicinal Chemistry. 46: 5628-37. PMID 14667217 DOI: 10.1021/Jm030060Q  0.767
2003 Fujii N, Haresco JJ, Novak KA, Stokoe D, Kuntz ID, Guy RK. A selective irreversible inhibitor targeting a PDZ protein interaction domain. Journal of the American Chemical Society. 125: 12074-5. PMID 14518976 DOI: 10.1021/Ja035540L  0.474
2003 Chong LT, Bandyopadhyay P, Scanlan TS, Kuntz ID, Kollman PA. Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. Journal of Computational Chemistry. 24: 1371-7. PMID 12868101 DOI: 10.1002/Jcc.10293  0.592
2003 Sullivan DC, Aynechi T, Voelz VA, Kuntz ID. Information content of molecular structures. Biophysical Journal. 85: 174-90. PMID 12829474 DOI: 10.1016/S0006-3495(03)74464-6  0.749
2003 Krumrine J, Raubacher F, Brooijmans N, Kuntz I. Principles and methods of docking and ligand design. Methods of Biochemical Analysis. 44: 443-76. PMID 12647399 DOI: 10.1002/0471721204.Ch22  0.677
2003 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. 68: 16-34. PMID 12579577 DOI: 10.1002/Bip.10270  0.45
2003 Brooijmans N, Kuntz ID. Molecular recognition and docking algorithms. Annual Review of Biophysics and Biomolecular Structure. 32: 335-73. PMID 12574069 DOI: 10.1146/Annurev.Biophys.32.110601.142532  0.66
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, et al. A novel mechanism for inhibition of HIV-1 reverse transcriptase. Bioorganic Chemistry. 30: 443-58. PMID 12642128 DOI: 10.1016/S0045-2068(02)00502-3  0.44
2002 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. Chemistry & Biology. 9: 1085-94. PMID 12401493 DOI: 10.1016/S1074-5521(02)00238-7  0.471
2002 Brooijmans N, Sharp KA, Kuntz ID. Stability of macromolecular complexes. Proteins. 48: 645-53. PMID 12211032 DOI: 10.1002/Prot.10139  0.69
2002 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. The Journal of Biological Chemistry. 277: 26623-31. PMID 11959867 DOI: 10.1074/Jbc.M203076200  0.364
2002 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. Journal of Medicinal Chemistry. 45: 1412-9. PMID 11906282 DOI: 10.1021/Jm010338J  0.499
2002 Sullivan DC, Kuntz ID. Protein folding as biased conformational diffusion Journal of Physical Chemistry B. 106: 3255-3262. DOI: 10.1021/Jp012911G  0.484
2001 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. The Journal of Biological Chemistry. 276: 34941-7. PMID 11438529 DOI: 10.1074/Jbc.M102997200  0.305
2001 Sullivan DC, Kuntz ID. Conformation spaces of proteins. Proteins. 42: 495-511. PMID 11170204 DOI: 10.1002/1097-0134(20010301)42:4<495::Aid-Prot80>3.0.Co;2-9  0.493
1999 Kuntz ID, Chen K, Sharp KA, Kollman PA. The maximal affinity of ligands. Proceedings of the National Academy of Sciences of the United States of America. 96: 9997-10002. PMID 10468550 DOI: 10.1073/Pnas.96.18.9997  0.452
1999 Wang J, Kollman PA, Kuntz ID. Flexible ligand docking: a multistep strategy approach. Proteins. 36: 1-19. PMID 10373002 DOI: 10.1002/(Sici)1097-0134(19990701)36:1<1::Aid-Prot1>3.0.Co;2-T  0.51
1999 Shoichet BK, Leach AR, Kuntz ID. Ligand solvation in molecular docking. Proteins. 34: 4-16. PMID 10336382 DOI: 10.1002/(Sici)1097-0134(19990101)34:1<4::Aid-Prot2>3.0.Co;2-6  0.525
1999 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. 38: 1607-17. PMID 9931028 DOI: 10.1021/Bi9815896  0.465
1997 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. Experimental Parasitology. 87: 212-21. PMID 9371086 DOI: 10.1006/Expr.1997.4220  0.493
1997 Knegtel RM, Kuntz ID, Oshiro CM. Molecular docking to ensembles of protein structures. Journal of Molecular Biology. 266: 424-40. PMID 9047373 DOI: 10.1006/jmbi.1996.0776  0.306
1996 Li R, Chen X, Gong B, Selzer PM, Li Z, Davidson E, Kurzban G, Miller RE, Nuzum EO, McKerrow JH, Fletterick RJ, Gillmor SA, Craik CS, Kuntz ID, Cohen FE, et al. Structure-based design of parasitic protease inhibitors. Bioorganic & Medicinal Chemistry. 4: 1421-7. PMID 8894100 DOI: 10.1016/0968-0896(96)00136-8  0.513
1996 Shoichet BK, Kuntz ID. Predicting the structure of protein complexes: a step in the right direction. Chemistry & Biology. 3: 151-6. PMID 8807840 DOI: 10.1016/S1074-5521(96)90256-2  0.487
1996 Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, et al. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nature Structural Biology. 3: 233-9. PMID 8605624 DOI: 10.1038/Nsb0396-233  0.483
1996 Stout TJ, Costi MP, Barlocco D, Rinaldi M, Shoichet B, Perry KM, Kuntz ID, Stroud RM. Structure-based discovery of a new class of enzyme inhibitors Acta Crystallographica Section a Foundations of Crystallography. 52: C207-C207. DOI: 10.1107/S0108767396091064  0.451
1996 Shah VJ, Cerpa R, Kuntz ID, Kenyon GL. Solid-phase synthesis of peptide-derived enantiospecific nucleic acid analogs Bioorganic Chemistry. 24: 201-206. DOI: 10.1006/Bioo.1996.0018  0.434
1996 Shah VJ, Kuntz ID, Kenyon GL. Synthesis of amino-acid-derived nucleo(side/tide) analogs for peptide- derived enantiospecific nucleic acid analogs Bioorganic Chemistry. 24: 194-200. DOI: 10.1006/Bioo.1996.0017  0.442
1995 Watts CR, Kerwin SM, Kenyon GL, Kuntz ID, Kallick DA. Rationally designed N,N′-bis[(N-p-guanidinobenzyl-N-methyl)aminocarbonyl]-1,3-diaminobenzene, "BIGBEN", binds to the minor groove of d(CGCGAATTCGCG)2 as determined by two-dimensional nuclear magnetic resonance spectroscopy Journal of the American Chemical Society. 117: 9941-9950. DOI: 10.1021/Ja00145A002  0.43
1994 Li Z, Chen X, Davidson E, Zwang O, Mendis C, Ring CS, Roush WR, Fegley G, Li R, Rosenthal PJ, Lee GK, Kenyon GL, Kuntz ID, Cohen FE. Anti-malarial drug development using models of enzyme structure Chemistry and Biology. 1: 31-37. PMID 9383368 DOI: 10.1016/1074-5521(94)90038-8  0.506
1994 Grootenhuis PD, Roe DC, Kollman PA, Kuntz ID. Finding potential DNA-binding compounds by using molecular shape. Journal of Computer-Aided Molecular Design. 8: 731-50. PMID 7738607 DOI: 10.1007/Bf00124018  0.407
1994 Kuntz ID, Meng EC, Shoichet BK. Structure-based molecular design Accounts of Chemical Research. 27: 117-123. DOI: 10.1021/Ar00041A001  0.496
1993 Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM. Structure-based discovery of inhibitors of thymidylate synthase. Science (New York, N.Y.). 259: 1445-50. PMID 8451640 DOI: 10.1126/Science.8451640  0.497
1993 Shoichet BK, Kuntz ID. Matching chemistry and shape in molecular docking. Protein Engineering. 6: 723-32. PMID 7504257 DOI: 10.1093/Protein/6.7.723  0.496
1992 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 Science : a Publication of the Protein Society. 1: 91-106. PMID 1284804 DOI: 10.1002/Pro.5560010110  0.464
1992 Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation Journal of Computational Chemistry. 13: 505-524. DOI: 10.1002/Jcc.540130412  0.52
1992 Shoichet BK, Kuntz ID, Bodian DL. Molecular docking using shape descriptors Journal of Computational Chemistry. 13: 380-397. DOI: 10.1002/Jcc.540130311  0.529
1991 Shoichet BK, Kuntz ID. Protein docking and complementarity. Journal of Molecular Biology. 221: 327-46. PMID 1920412 DOI: 10.1016/0022-2836(91)80222-G  0.53
1991 Daggett V, Kollman PA, Kuntz ID. Molecular dynamics simulations of small peptides: dependence on dielectric model and pH. Biopolymers. 31: 285-304. PMID 1868159 DOI: 10.1002/Bip.360310304  0.591
1991 Daggett V, Kollman PA, Kuntz ID. A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers. 31: 1115-34. PMID 1786342 DOI: 10.1002/Bip.360310911  0.61
1990 Grootenhuis PD, Kollman PA, Seibel GL, DesJarlais RL, Kuntz ID. Computerized selection of potential DNA binding compounds. Anti-Cancer Drug Design. 5: 237-42. PMID 2169249  0.417
1990 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. Bio/Technology (Nature Publishing Company). 8: 945-9. PMID 1370005 DOI: 10.1038/Nbt1090-945  0.626
1988 Tilton RF, Singh UC, Kuntz ID, Kollman PA. Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex. Journal of Molecular Biology. 199: 195-211. PMID 3351919 DOI: 10.1016/0022-2836(88)90389-0  0.459
1986 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 Journal of Molecular Biology. 192: 443-456. PMID 3560222 DOI: 10.1016/0022-2836(86)90374-8  0.487
1986 Cohen FE, Kosen PA, Kuntz ID, Epstein LB, Ciardelli TL, Smith KA. Structure-activity studies of interleukin-2 Science. 234: 349-352. PMID 3489989 DOI: 10.1126/Science.3489989  0.313
1986 Babbitt PC, Kenyon GL, Kuntz ID, Cohen FE, Baxter JD, Benfield PA, Buskin JD, Gilbert WA, Hauschka SD, Hossle JP, Ordahl CP, Pearson ML, Perriard JC, Pickering LA, Putney SD, et al. Comparisons of creatine kinase primary structures Journal of Protein Chemistry. 5: 1-14. DOI: 10.1007/Bf01025580  0.645
1983 Havel TF, Kuntz ID, Crippen GM. The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem Journal of Theoretical Biology. 104: 359-381. PMID 6656266 DOI: 10.1016/0022-5193(83)90112-1  0.576
1983 Havel TF, Crippen GM, Kuntz ID, Blaney JM. The combinatorial distance geometry method for the calculation of molecular conformation II. Sample problems and computational statistics Journal of Theoretical Biology. 104: 383-400. PMID 6197591 DOI: 10.1016/0022-5193(83)90113-3  0.573
1983 Weiner PK, Profeta S, Wipff G, Havel T, Kuntz ID, Langridge R, Kollman PA. A distance geometry study of ring systems. Application to cyclooctane, 18-crown-6, cyclododecane and androstanedione Tetrahedron. 39: 1113-1121. DOI: 10.1016/S0040-4020(01)91874-5  0.47
1980 Cohen FE, Sternberg MJ, Phillips DC, Kuntz ID, Kollman PA. A diffusion--collision--adhesion model for the kinetics of myoglobin refolding. Nature. 286: 632-4. PMID 7402344 DOI: 10.1038/286632A0  0.398
1980 Connolly ML, Kuntz ID, Crippen GM. Linked and threaded loops in proteins Biopolymers - Peptide Science Section. 19: 1167-1182. PMID 7378549  0.557
1980 Kuntz ID, Crippen GM. A computer model for the 30S ribosome subunit Biophysical Journal. 32: 677-695. PMID 7020786  0.589
1979 Kuntz ID, Crippen GM. Protein densities International Journal of Peptide and Protein Research. 13: 223-228. PMID 429098  0.547
1979 Kuntz ID, Crippen GM, Kollman PA. Application of distance geometry to protein tertiary structure calculations Biopolymers. 18: 939-957. DOI: 10.1002/Bip.1979.360180414  0.518
1978 Crippen GM, Kuntz ID. A survey of atom packing in globular proteins International Journal of Peptide and Protein Research. 12: 47-56. PMID 681085  0.56
1978 Wolff ME, Baxter JD, Kollman PA, Lee DL, Kuntz ID, Bloom E, Matulich DT, Morris J. Nature of steroid-glucocorticoid receptor interactions: thermodynamic analysis of the binding reaction. Biochemistry. 17: 3201-8. PMID 567487 DOI: 10.1021/Bi00609A005  0.383
1977 Crippen GM, Kuntz ID. Directional structural features of globular proteins Journal of Theoretical Biology. 66: 47-61. PMID 875421 DOI: 10.1016/0022-5193(77)90311-3  0.574
1977 Kollman P, Kuntz I. Additions and Corrections - Hydration of NH4F Journal of the American Chemical Society. 99: 3894-3894. DOI: 10.1021/Ja00453A603  0.435
1977 KOLLMAN P, KUNTZ I. ChemInform Abstract: HYDRATION OF AMMONIUM FLUORIDE Chemischer Informationsdienst. 8: no-no. DOI: 10.1002/Chin.197705003  0.418
1976 Kuntz ID, Crippen GM, Kollman PA, Kimelman D. Calculation of protein tertiary structure Journal of Molecular Biology. 106: 983-994. PMID 978745 DOI: 10.1016/0022-2836(76)90347-8  0.683
1976 Kollman P, Kuntz I. Hydration of ammonium fluoride Journal of the American Chemical Society. 98: 6820-6825. DOI: 10.1021/Ja00438A007  0.418
1974 Kollman PA, Kuntz ID. Hydration number of lithium(1+) ion Journal of the American Chemical Society. 96: 4766-4769. DOI: 10.1021/Ja00822A007  0.327
1973 KOLLMAN PA, KUNTZ ID. ChemInform Abstract: HYDRATATION VON KATIONEN Chemischer Informationsdienst. 4: no-no. DOI: 10.1002/Chin.197310019  0.343
1969 Johnston MD, Gasparro FP, Kuntz ID. Nuclear magnetic resonance solvent effects and molecular inter-actions. II. A comparison of dipolar, hydrogen-bonding, and charge-transfer effects Journal of the American Chemical Society. 91: 5715-5724. DOI: 10.1021/ja01049a004  0.543
1968 Kuntz ID, Gasparro FP, Johnston MD, Taylor RP. Molecular interactions and the Benesi-Hildebrand equation Journal of the American Chemical Society. 90: 4778-4781. DOI: 10.1021/ja01020a004  0.541
1965 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. Photochemistry and Photobiology. 4: 483-90. PMID 5873425 DOI: 10.1111/J.1751-1097.1965.Tb09764.X  0.347
1965 Kuntz ID, Calvin M. KINETIC STUDIES OF THE TWO LIGHT REACTIONS IN PHOTOSYNTHESIS Photochemistry and Photobiology. 4: 537-548. DOI: 10.1111/j.1751-1097.1965.tb09771.x  0.323
1964 RUBY RH, KUNTZ ID, CALVIN M. A CONTRIBUTION TO THE UNDERSTANDING OF THE PRIMARY QUANTUM CONVERSION IN PHOTOSYNTHESIS. UCRL-11212. Ucrl [Reports]. U.S. Atomic Energy Commission. 36: 1-19. PMID 24547359  0.323
1964 RUBY RH, KUNTZ ID, CALVIN M. A CONTRIBUTION TO THE UNDERSTANDING OF THE PRIMARY QUANTUM CONVERSION IN PHOTOSYNTHESIS. Bulletin De La SociéTé De Chimie Biologique. 46: 1595-605. PMID 14270542  0.323
1964 KUNTZ ID, LOACH PA, CALVIN M. ABSORPTION CHANGES IN BACTERIAL CHROMATOPHORES. Biophysical Journal. 4: 227-49. PMID 14185583 DOI: 10.1016/S0006-3495(64)86779-5  0.351
1964 RUBY RH, KUNTZ ID, CALVIN M. TRANSIENT EPR AND ABSORBENCE CHANGES IN PHOTPSYNTHETIC BACTERIA. Proceedings of the National Academy of Sciences of the United States of America. 51: 515-20. PMID 14171949 DOI: 10.1073/Pnas.51.3.515  0.304
Low-probability matches (unlikely to be authored by this person)
1989 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. 28: 7516-7523. PMID 2558710 DOI: 10.1021/Bi00445A004  0.299
2005 Lang PT, Kuntz ID, Maggiora GM, Bajorath J. Evaluating the high-throughput screening computations. Journal of Biomolecular Screening. 10: 649-52. PMID 16170047 DOI: 10.1177/1087057105281269  0.291
1996 Gschwend DA, Good AC, Kuntz ID. Molecular docking towards drug discovery. Journal of Molecular Recognition : Jmr. 9: 175-86. PMID 8877811 DOI: 10.1002/(SICI)1099-1352(199603)9:2<175::AID-JMR260>3.0.CO;2-D  0.284
1996 Briem H, Kuntz ID. Molecular similarity based on DOCK-generated fingerprints. Journal of Medicinal Chemistry. 39: 3401-8. PMID 8765524 DOI: 10.1021/jm950800y  0.259
1987 Cohen FE, Kuntz ID. Prediction of the three-dimensional structure of human growth hormone Proteins: Structure, Function and Genetics. 2: 162-166. PMID 3447173  0.252
1988 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. Journal of Medicinal Chemistry. 31: 722-9. PMID 3127588  0.246
1982 Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology. 161: 269-88. PMID 7154081 DOI: 10.1016/0022-2836(82)90153-X  0.245
2004 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. Journal of Medicinal Chemistry. 47: 3065-74. PMID 15163188 DOI: 10.1021/Jm030570K  0.242
2004 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. Journal of Chemical Information and Computer Sciences. 44: 2190-8. PMID 15554689 DOI: 10.1021/ci049814f  0.239
1984 Tilton RF, Kuntz ID, Petsko GA. Cavities in proteins: Structure of a metmyoglobin-xenon complex solved to 1.9 Å Biochemistry. 23: 2849-2857. PMID 6466620 DOI: 10.1021/Bi00308A002  0.236
1998 Oshiro CM, Kuntz ID. Characterization of receptors with a new negative image: use in molecular docking and lead optimization. Proteins. 30: 321-36. PMID 9517547 DOI: 10.1002/(SICI)1097-0134(19980215)30:3<321::AID-PROT11>3.0.CO;2-H  0.236
1997 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. Bioorganic & Medicinal Chemistry. 5: 2019-27. PMID 9416419 DOI: 10.1016/S0968-0896(97)00131-4  0.234
1990 Kuntz I. Applications and extensions of dock Journal of Molecular Graphics. 8: 233. DOI: 10.1016/0263-7855(90)80021-7  0.232
1993 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. Proceedings of the National Academy of Sciences of the United States of America. 90: 3583-7. PMID 8475107 DOI: 10.1073/Pnas.90.8.3583  0.232
1984 Rosevear PR, Sellin S, Mannervik B, Kuntz ID, Mildvan AS. NMR and computer modeling studies of the conformations of glutathione derivatives at the active site of glyoxalase I. The Journal of Biological Chemistry. 259: 11436-47. PMID 6547959  0.232
2001 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. 42: 296-318. PMID 11151003 DOI: 10.1002/1097-0134(20010215)42:3<296::AID-PROT20>3.0.CO;2-F  0.227
1995 Good AC, Kuntz ID. Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors. Journal of Computer-Aided Molecular Design. 9: 373-9. PMID 8523046 DOI: 10.1007/BF00125178  0.223
1993 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. The Journal of Biological Chemistry. 268: 15343-6. PMID 8340363  0.22
1995 Oshiro CM, Kuntz ID, Dixon JS. Flexible ligand docking using a genetic algorithm. Journal of Computer-Aided Molecular Design. 9: 113-30. PMID 7608743 DOI: 10.1007/BF00124402  0.219
1997 Kick EK, Roe DC, Skillman AG, Liu G, Ewing TJ, Sun Y, Kuntz ID, Ellman JA. Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D. Chemistry & Biology. 4: 297-307. PMID 9195867 DOI: 10.1016/S1074-5521(97)90073-9  0.219
1994 Yamamoto Y, Ishihara Y, Kuntz ID. Docking analysis of a series of benzylamino acetylcholinesterase inhibitors with a phthalimide, benzoyl, or indanone moiety. Journal of Medicinal Chemistry. 37: 3141-53. PMID 7932538  0.218
2006 Verras A, Kuntz ID, Ortiz de Montellano PR. Chapter 10 Cytochrome P450 Enzymes: Computational Approaches to Substrate Prediction Annual Reports in Computational Chemistry. 2: 171-195. DOI: 10.1016/S1574-1400(06)02010-X  0.218
1961 Taylor EC, Paudler WW, Kuntz I. A PHOTOCHEMICALLY-INDUCED, VALENCE-BOND TAUTOMERISM IN A SIX-MEMBERED AROMATIC SYSTEM Journal of the American Chemical Society. 83: 2967-2968. DOI: 10.1021/Ja01474A053  0.217
2000 Siani MA, Skillman AG, Carreras CW, Ashley G, Kuntz ID, Santi DV. Development and screening of a polyketide virtual library for drug leads against a motilide pharmacophore. Journal of Molecular Graphics & Modelling. 18: 497-511, 539-40. PMID 11143565 DOI: 10.1016/S1093-3263(00)00070-X  0.217
2004 Kang X, Shafer RH, Kuntz ID. Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK. Biopolymers. 73: 192-204. PMID 14755577 DOI: 10.1002/Bip.10541  0.214
1999 Young MM, Skillman AG, Kuntz ID. A rapid method for exploring the protein structure universe. Proteins. 34: 317-32. PMID 10024019 DOI: 10.1002/(SICI)1097-0134(19990215)34:3<317::AID-PROT5>3.0.CO;2-7  0.213
1991 Oshiro CM, Thomason J, Kuntz ID. Effects of limited input distance constraints upon the distance geometry algorithm. Biopolymers. 31: 1049-64. PMID 1786338 DOI: 10.1002/bip.360310905  0.213
1994 Meng EC, Kuntz ID, Abraham DJ, Kellogg GE. Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities. Journal of Computer-Aided Molecular Design. 8: 299-306. PMID 7964929 DOI: 10.1007/Bf00126747  0.212
1992 Kuntz ID. Structure-based strategies for drug design and discovery. Science (New York, N.Y.). 257: 1078-82. PMID 1509259  0.208
1993 Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid-body minimization in molecular docking. Proteins. 17: 266-78. PMID 8272425 DOI: 10.1002/prot.340170305  0.207
1997 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. 29: 59-67. PMID 9294866 DOI: 10.1002/(SICI)1097-0134(199709)29:1<59::AID-PROT4>3.0.CO;2-A  0.207
1998 Hendrix DK, Kuntz ID. Surface solid angle-based site points for molecular docking. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 317-26. PMID 9697192  0.206
1995 Good AC, Ewing TJ, Gschwend DA, Kuntz ID. New molecular shape descriptors: application in database screening. Journal of Computer-Aided Molecular Design. 9: 1-12. PMID 7751866 DOI: 10.1007/BF00117274  0.203
1999 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 Science : a Publication of the Protein Society. 8: 1010-22. PMID 10338012 DOI: 10.1110/ps.8.5.1010  0.201
1998 Marino S, Kuntz ID. ELECT + + : Faster conformational search method for docking flexible molecules using molecular similarity Journal of Computational Chemistry. 19: 1834-1852.  0.201
1991 Hurle MR, Anderson S, Kuntz ID. Confirmation of the predicted source of a slow folding reaction: proline 8 of bovine pancreatic trypsin inhibitor. Protein Engineering. 4: 451-5. PMID 1881870  0.2
2001 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. Antimicrobial Agents and Chemotherapy. 45: 2571-6. PMID 11502531 DOI: 10.1128/AAC.45.9.2571-2576.2001  0.2
1994 Meng EC, Kuntz ID. Molecular docking: A tool for ligand discovery and design Drug Information Journal. 28: 733-749.  0.2
1999 Haque TS, Skillman AG, Lee CE, Habashita H, Gluzman IY, Ewing TJ, Goldberg DE, Kuntz ID, Ellman JA. Potent, low-molecular-weight non-peptide inhibitors of malarial aspartyl protease plasmepsin II. Journal of Medicinal Chemistry. 42: 1428-40. PMID 10212129 DOI: 10.1021/Jm980641T  0.2
1986 DesJarlais RL, Sheridan RP, Dixon JS, Kuntz ID, Venkataraghavan R. Docking flexible ligands to macromolecular receptors by molecular shape Journal of Medicinal Chemistry. 29: 2149-2153. PMID 3783576  0.199
1992 Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID. Automated site-directed drug design using molecular lattices. Journal of Molecular Graphics. 10: 66-78, 106. PMID 1637751 DOI: 10.1016/0263-7855(92)80059-M  0.196
1993 Oshiro CM, Kuntz ID. Application of distance geometry to the proton assignment problem. Biopolymers. 33: 107-15. PMID 8381306 DOI: 10.1002/bip.360330110  0.196
1999 Zou X, Sun Y, Kuntz ID. Inclusion of solvation in ligand binding free energy calculations using the generalized-born model Journal of the American Chemical Society. 121: 8033-8043. DOI: 10.1021/ja984102p  0.196
2010 Kuntz ID. Structures of proteins. Science (New York, N.Y.). 210: 420. PMID 17837421 DOI: 10.1126/science.210.4468.420  0.193
2004 Verras A, Kuntz ID, Ortiz de Montellano PR. Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes. Journal of Medicinal Chemistry. 47: 3572-9. PMID 15214784 DOI: 10.1021/Jm030608T  0.192
2001 Ewing TJ, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. Journal of Computer-Aided Molecular Design. 15: 411-28. PMID 11394736 DOI: 10.1023/A:1011115820450  0.192
2000 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. 39: 4684-91. PMID 10769124 DOI: 10.1021/bi992555g  0.188
2000 Hopkins SC, Vale RD, Kuntz ID. Inhibitors of kinesin activity from structure-based computer screening. Biochemistry. 39: 2805-14. PMID 10704233 DOI: 10.1021/Bi992474K  0.187
1988 Billeter M, Howard AE, Kuntz ID, Kollman PA. A new technique to calculate low-energy conformations of cyclic molecules utilizing the ellipsoid algorithm and molecular dynamics: Application to 18-crown-6 Journal of the American Chemical Society. 110: 8385-8391.  0.186
1981 Langridge R, Ferrin TE, Kuntz ID, Connolly ML. Real-time color graphics in studies of molecular interactions. Science (New York, N.Y.). 211: 661-6. PMID 7455704 DOI: 10.1126/Science.7455704  0.185
1995 Chapman BS, Kuntz ID. Modeled structure of the 75-kDa neurotrophin receptor. Protein Science : a Publication of the Protein Society. 4: 1696-707. PMID 8528068 DOI: 10.1002/pro.5560040905  0.185
1998 Sun Y, Ewing TJ, Skillman AG, Kuntz ID. CombiDOCK: structure-based combinatorial docking and library design. Journal of Computer-Aided Molecular Design. 12: 597-604. PMID 9879507  0.183
1997 Chen Q, Shafer RH, Kuntz ID. Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry. 36: 11402-7. PMID 9298959 DOI: 10.1021/Bi970756J  0.183
1996 Gschwend DA, Kuntz ID. Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal. Journal of Computer-Aided Molecular Design. 10: 123-32. PMID 8741016  0.182
1975 Kuntz ID. An approach to the tertiary structure of globular proteins Journal of the American Chemical Society. 97: 4362-4366. PMID 1141597  0.182
1995 Benjamin DR, Markby DW, Bourne HR, Kuntz ID. Solution structure of the GTPase activating domain of alpha s. Journal of Molecular Biology. 254: 681-91. PMID 7500342 DOI: 10.1006/Jmbi.1995.0647  0.181
1990 Guiles RD, Altman J, Kuntz ID, Waskell L. Structural studies of cytochrome b5: Complete sequence-specific resonance assignments for the trypsin-solubilized microsomal ferrocytochrome b5 obtained from pig and calf Biochemistry. 29: 1276-1289. PMID 2322562 DOI: 10.1021/Bi00457A025  0.18
1987 Marks CB, Naderi H, Kosen PA, Kuntz ID, Anderson S. Mutants of bovine pancreatic trypsin inhibitor lacking cysteines 14 and 38 can fold properly. Science (New York, N.Y.). 235: 1370-3. PMID 2435002 DOI: 10.1126/science.2435002  0.178
1989 Cohen FE, Gregoret L, Presnell SR, Kuntz ID. Protein structure predictions: new theoretical approaches. Progress in Clinical and Biological Research. 289: 75-85. PMID 2657754  0.178
1984 Blanar MA, Kneller D, Clark AJ, Karu AE, Cohen FE, Langridge R, Kuntz ID. A model for the core structure of the Escherichia coli RecA protein. Cold Spring Harbor Symposia On Quantitative Biology. 49: 507-11. PMID 6397305 DOI: 10.1101/Sqb.1984.049.01.057  0.175
1996 Guiles RD, Sarma S, DiGate RJ, Banville D, Basus VJ, Kuntz ID, Waskell L. Pseudocontact shifts used in the restraint of the solution structures of electron transfer complexes. Nature Structural Biology. 3: 333-9. PMID 8599759 DOI: 10.1038/nsb0496-333  0.172
1986 Cohen FE, Abarbanel RM, Kuntz ID, Fletterick RJ. Turn prediction in proteins using a pattern-matching approach Biochemistry. 25: 266-275. PMID 3754149 DOI: 10.1021/Bi00349A037  0.17
2001 Pegg SC, Haresco JJ, Kuntz ID. A genetic algorithm for structure-based de novo design. Journal of Computer-Aided Molecular Design. 15: 911-33. PMID 11918076 DOI: 10.1023/A:1014389729000  0.17
2002 Guo X, Schilling B, Young M, Medzihradszky M, Kuntz ID, Guy RK, Gibson BW. Using homobifunctional crosslinking reagents with normal and N-15 labeled proteins for the determination of protein tertiary structure and protein-protein interactions Proceedings 50th Asms Conference On Mass Spectrometry and Allied Topics. 249-250.  0.17
1999 Makino S, Ewing TJ, Kuntz ID. DREAM++: flexible docking program for virtual combinatorial libraries. Journal of Computer-Aided Molecular Design. 13: 513-32. PMID 10483532 DOI: 10.1023/A:1008066310669  0.168
1991 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 Engineering. 4: 593-600. PMID 1716367  0.167
2000 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. Proceedings of the National Academy of Sciences of the United States of America. 97: 5802-6. PMID 10811876 DOI: 10.1073/Pnas.090099097  0.166
1992 Bemis GW, Kuntz ID. A fast and efficient method for 2D and 3D molecular shape description. Journal of Computer-Aided Molecular Design. 6: 607-28. PMID 1291629 DOI: 10.1007/BF00126218  0.165
1996 Chen Q, Kuntz ID, Shafer RH. Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye. Proceedings of the National Academy of Sciences of the United States of America. 93: 2635-9. PMID 8610093 DOI: 10.1073/Pnas.93.7.2635  0.165
2002 Schilling B, Collins CJ, Young MM, Guo X, Kuntz ID, Leavitt AD, Guy K, Gibson BW. Chemical cross-linking strategies to determine protein conformation using a combinatorial set of cross-linking reagents Proceedings 50th Asms Conference On Mass Spectrometry and Allied Topics. 125-126.  0.162
1987 Hurle MR, Matthews CR, Cohen FE, Kuntz ID, Toumadje A, Johnson WC. Prediction of the tertiary structure of the α-subunit of tryptophan synthase Proteins: Structure, Function and Genetics. 2: 210-224. PMID 3328862 DOI: 10.1002/Prot.340020306  0.161
1995 Roe DC, Kuntz ID. BUILDER v.2: improving the chemistry of a de novo design strategy. Journal of Computer-Aided Molecular Design. 9: 269-82. PMID 7561978 DOI: 10.1007/BF00124457  0.16
1997 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. Journal of Virology. 71: 8808-20. PMID 9343241 DOI: 10.1128/Jvi.71.11.8808-8820.1997  0.159
1997 Makino S, Kuntz ID. Automated flexible ligand docking method and its application for database search Journal of Computational Chemistry. 18: 1812-1825.  0.158
1992 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. 31: 5705-17. PMID 1377024  0.153
1990 Bradley EK, Thomason JF, Cohen FE, Kosen PA, Kuntz ID. Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance. Journal of Molecular Biology. 215: 607-22. PMID 2231722 DOI: 10.1016/S0022-2836(05)80172-X  0.151
1973 Kuntz ID. Tertiary structure in carboxypeptidase. Journal of the American Chemical Society. 94: 8568-72. PMID 4638988 DOI: 10.1021/ja00779a046  0.15
1993 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. 32: 2967-78. PMID 8457561  0.148
1992 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. 31: 11365-75. PMID 1332756 DOI: 10.1021/Bi00161A014  0.148
1987 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. 26: 254-61. PMID 3828301 DOI: 10.1021/Bi00375A035  0.147
1985 Gariépy J, Kay LE, Kuntz ID, Sykes BD, Hodges RS. Nuclear magnetic resonance determination of metal-proton distances in a synthetic calcium binding site of rabbit skeletal troponin C Biochemistry. 24: 544-550. PMID 2983759 DOI: 10.1021/Bi00323A045  0.147
1988 Bashford D, Cohen FE, Karplus M, Kuntz ID, Weaver DL. Diffusion-collision model for the folding kinetics of myoglobin. Proteins. 4: 211-27. PMID 3237719 DOI: 10.1002/Prot.340040308  0.147
1974 Kuntz ID, Kauzmann W. Hydration of Proteins and Polypeptides Advances in Protein Chemistry. 28: 239-345. DOI: 10.1016/S0065-3233(08)60232-6  0.146
1983 Cohen FE, Abarbanel RM, Kuntz ID, Fletterick RJ. Secondary structure assignment for α/β proteins by a combinatorial approach Biochemistry. 22: 4894-4904. PMID 6639935 DOI: 10.1021/Bi00290A005  0.145
1988 Basus VJ, Billeter M, Love RA, Stroud RM, Kuntz ID. Structural studies of alpha-bungarotoxin. 1. Sequence-specific 1H NMR resonance assignments. Biochemistry. 27: 2763-71. PMID 3401447 DOI: 10.1021/Bi00408A016  0.144
1986 Argaraña CE, Kuntz ID, Birken S, Axel R, Cantor CR. Molecular cloning and nucleotide sequence of the streptavidin gene. Nucleic Acids Research. 14: 1871-82. PMID 3951999 DOI: 10.1093/Nar/14.4.1871  0.144
1992 Leach AR, Kuntz ID. Conformational analysis of flexible ligands in macromolecular receptor sites Journal of Computational Chemistry. 13: 730-748. DOI: 10.1002/jcc.540130608  0.143
1972 Kuntz ID. Protein folding. Journal of the American Chemical Society. 94: 4009-12. PMID 5037986 DOI: 10.1021/ja00766a060  0.143
2001 Bressi JC, Verlinde CL, Aronov AM, Shaw ML, Shin SS, Nguyen LN, Suresh S, Buckner FS, Van Voorhis WC, Kuntz ID, Hol WG, Gelb MH. Adenosine analogues as selective inhibitors of glyceraldehyde-3-phosphate dehydrogenase of Trypanosomatidae via structure-based drug design. Journal of Medicinal Chemistry. 44: 2080-93. PMID 11405646 DOI: 10.1021/Jm000472O  0.143
2000 Bi X, Haque TS, Zhou J, Skillman AG, Lin B, Lee CE, Kuntz ID, Ellman JA, Lynch G. Novel cathepsin D inhibitors block the formation of hyperphosphorylated tau fragments in hippocampus. Journal of Neurochemistry. 74: 1469-77. PMID 10737603 DOI: 10.1046/J.1471-4159.2000.0741469.X  0.143
1990 Lewis RA, Kuntz ID. Chapter 11 Site-Directed Computer-Aided Drug Design: Progress Towards the Design of Novel Lead Compounds Using 'Molecular' Lattices Data Handling in Science and Technology. 6: 117-132. DOI: 10.1016/S0922-3487(08)70161-8  0.142
1995 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. 34: 155-62. PMID 7819191  0.14
1993 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. 32: 8329-40. PMID 8347629 DOI: 10.1021/Bi00083A037  0.139
1998 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. 37: 5344-8. PMID 9548915 DOI: 10.1021/Bi973095Z  0.135
2004 Liu HY, Kuntz ID, Zou X. Pairwise GB/SA scoring function for structure-based drug design Journal of Physical Chemistry B. 108: 5453-5462.  0.135
1996 Cerpa R, Cohen FE, Kuntz ID. Conformational switching in designed peptides: the helix/sheet transition. Folding & Design. 1: 91-101. PMID 9079369 DOI: 10.1016/S1359-0278(96)00018-1  0.132
1979 Havel TF, Crippen GM, Kuntz ID. Effects of distance constraints on macromolecular conformation. II. Simulation of experimental results and theoretical predictions Biopolymers. 18: 73-81. DOI: 10.1002/bip.1979.360180108  0.131
2008 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. Journal of Proteome Research. 7: 4848-57. PMID 18817429 DOI: 10.1021/Pr800443F  0.13
1985 Sheridan RP, Dixon JS, Venkataraghavan R, Kuntz ID, Scott KP. Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures Biopolymers. 24: 1995-2023. PMID 4074850 DOI: 10.1002/bip.360241011  0.129
1993 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. The Journal of Cell Biology. 123: 1149-60. PMID 8245123 DOI: 10.1083/Jcb.123.5.1149  0.128
1997 Ewing TJA, Kuntz ID. Critical evaluation of search algorithms for automated molecular docking and database screening Journal of Computational Chemistry. 18: 1175-1189.  0.127
2012 Kuntz ID. Darwinian docking. Journal of Computer-Aided Molecular Design. 26: 73-5. PMID 22143893 DOI: 10.1007/s10822-011-9503-4  0.123
1971 Kuntz ID, Brassfield TS. Hydration of macromolecules. II. Effects of urea on protein hydration. Archives of Biochemistry and Biophysics. 142: 660-4. PMID 5550166 DOI: 10.1016/0003-9861(71)90532-7  0.12
1982 Tilton RF, Kuntz ID. Nuclear magnetic resonance studies of xenon-129 with myoglobin and hemoglobin Biochemistry. 21: 6850-6857. PMID 7159568  0.12
1990 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. 29: 4410-9. PMID 1693524  0.12
1991 Kuntz ID, Kosen PA, Craig EC. Amide chemical shifts in many helices in peptides and proteins are periodic Journal of the American Chemical Society. 113: 1406-1408.  0.119
1991 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. Advances in Experimental Medicine and Biology. 306: 489-92. PMID 1812747 DOI: 10.1007/978-1-4684-6012-4_62  0.118
1990 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. Proceedings of the National Academy of Sciences of the United States of America. 87: 6644-8. PMID 2204060 DOI: 10.1073/Pnas.87.17.6644  0.114
1986 Kosen PA, Scheek RM, Naderi H, Basus VJ, Manogaran S, Schmidt PG, Oppenheimer NJ, Kuntz ID. Two-dimensional 1H NMR of three spin-labeled derivatives of bovine pancreatic trypsin inhibitor. Biochemistry. 25: 2356-64. PMID 2424497 DOI: 10.1021/Bi00357A009  0.113
1991 Nilsson B, Berman-Marks C, Kuntz ID, Anderson S. Secretion incompetence of bovine pancreatic trypsin inhibitor expressed in Escherichia coli. The Journal of Biological Chemistry. 266: 2970-7. PMID 1704370  0.112
1969 Kuntz ID, Brassfield TS, Law GD, Purcell GV. Hydration of macromolecules. Science (New York, N.Y.). 163: 1329-31. PMID 5765111 DOI: 10.1126/science.163.3873.1329  0.111
2003 Kuntz ID, Agard DA. Assessment of the role of computations in structural biology. Advances in Protein Chemistry. 66: 1-25. PMID 14631815 DOI: 10.1016/S0065-3233(03)66001-8  0.111
1987 Billeter M, Havel TF, Kuntz ID. A new approach to the problem of docking two molecules: the ellipsoid algorithm. Biopolymers. 26: 777-93. PMID 3607242 DOI: 10.1002/bip.360260602  0.109
1996 McPhee F, Good AC, 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. 93: 11477-81. PMID 8876160 DOI: 10.1073/Pnas.93.21.11477  0.109
1971 Kuntz ID. Hydration of macromolecules. IV. Polypeptide conformation in frozen solutions. Journal of the American Chemical Society. 93: 516-8. PMID 5541519 DOI: 10.1021/ja00731a037  0.101
1996 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. The Biochemical Journal. 320: 681-6. PMID 8973584 DOI: 10.1042/Bj3200681  0.1
1987 Kuntz ID. Macromolecular structure in solution. Protein Engineering. 1: 147-8. PMID 3507700  0.098
1989 Eads CD, Kuntz ID. Programs for computer-assisted sequential assignment of proteins Journal of Magnetic Resonance (1969). 82: 467-482. DOI: 10.1016/0022-2364(89)90210-2  0.097
1990 Guiles RD, Altman J, Lipka JJ, Kuntz ID, Waskell L. Structural studies of cytochrome b5: complete sequence-specific resonance assignments for the trypsin-solubilized microsomal ferrocytochrome b5 obtained from pig and calf [Erratum to document cited in CA112(9):72477q] Biochemistry. 29: 11146-11146. DOI: 10.1021/Bi00502A020  0.093
1967 Kuntz ID, Johnston MD. Nuclear magnetic resonance solvent effects and molecular interactions Journal of the American Chemical Society. 89: 6008-6017. DOI: 10.1021/ja01000a003  0.092
1996 Yu Z, Caldera P, McPhee F, De Voss JJ, Jones PR, Burlingame AL, Kuntz ID, Craik CS, Ortiz De Montellano PR. Irreversible inhibition of the HIV-1 protease: Targeting alkylating agents to the catalytic aspartate groups Journal of the American Chemical Society. 118: 5846-5856. DOI: 10.1021/Ja954069W  0.092
2004 Chambers JJ, Gouda H, Young DM, Kuntz ID, England PM. Photochemically knocking out glutamate receptors in vivo. Journal of the American Chemical Society. 126: 13886-7. PMID 15506725 DOI: 10.1021/ja048331p  0.087
1989 Kuntz ID, Thomason JF, Oshiro CM. Distance geometry. Methods in Enzymology. 177: 159-204. PMID 2607979 DOI: 10.1016/0076-6879(89)77011-7  0.086
2005 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. Proceedings of the National Academy of Sciences of the United States of America. 102: 18700-5. PMID 16344478 DOI: 10.1073/Pnas.0508693102  0.083
1971 Kuntz ID. Hydration of macromolecules. III. Hydration of polypeptides Journal of the American Chemical Society. 93: 514-516. DOI: 10.1021/ja00731a036  0.08
1978 James TL, Matson GB, Kuntz ID. Protein rotational correlation times determined in aqueous solution by carbon-13 rotating frame spin-lattice relaxation in the presence of an off-resonance radiofrequency field Journal of the American Chemical Society. 100: 3590-3594. DOI: 10.1021/Ja00479A049  0.079
1975 Sawyer HW, Dabscheck R, Nott PR, Selinger BK, Kuntz ID. Hydrodynamic changes accompanying the loss of metal ions from concanavalin A Biochemical Journal. 147: 613-615. PMID 241332  0.077
1972 White JP, Kuntz ID, Cantor CR. Studies on the hydration of Escherichia coli ribosomes by nuclear magnetic resonance. Journal of Molecular Biology. 64: 511-4. PMID 4554021 DOI: 10.1016/0022-2836(72)90514-1  0.073
1976 Zipp A, James TL, Kuntz ID, Shohet SB. Water proton magnetic resonance studies of normal and sickle erythrocytes Temperature and volume dependence Bba - General Subjects. 428: 291-303. PMID 1276160 DOI: 10.1016/0304-4165(76)90037-4  0.071
1975 Kuntz ID, Cheng CJ. Infrared studies of water-ion interactions in aprotic solvents Journal of the American Chemical Society. 97: 4852-4859.  0.07
1988 Milder SJ, Bjorling SC, Kuntz ID, Kliger DS. Time-resolved circular dichroism and absorption studies of the photolysis reaction of (carbonmonoxy)myoglobin. Biophysical Journal. 53: 659-64. PMID 3390516 DOI: 10.1016/S0006-3495(88)83146-1  0.07
1993 Zhang CF, Lewis JW, Cerpa R, Kuntz ID, Kliger DS. Nanosecond circular dichroism spectral measurements: Extension to the far-ultraviolet region Journal of Physical Chemistry. 97: 5499-5505. DOI: 10.1021/J100123A009  0.067
1977 James TL, Matson GB, Kuntz ID, Fisher RW, Buttlaire DH. Rotating frame spin-lattice relaxation in the presence of an off-resonance radio frequency field. Investigation of intermediate molecular motions Journal of Magnetic Resonance (1969). 28: 417-426. DOI: 10.1016/0022-2364(77)90283-9  0.064
1999 Vaz RJ, Kuntz ID, Meng EC. Evaluating non-bonded parameters for zinc in DOCK Medicinal Chemistry Research. 9: 479-489.  0.059
1988 Billeter M, Basus VJ, Kuntz ID. A program for semi-automatic sequential resonance assignments in protein 1H nuclear magnetic resonance spectra Journal of Magnetic Resonance (1969). 76: 400-415. DOI: 10.1016/0022-2364(88)90346-0  0.059
1970 Kuntz ID, Taylor RP. Ionic interactions in solution. II. Infrared studies The Journal of Physical Chemistry. 74: 4573-4577. DOI: 10.1021/J100720A019  0.058
1976 Zipp A, Kuntz ID, James TL. An investigation of "bound" water in frozen erythrocytes by proton magnetic resonance spin-lattice, spin-spin, and rotating frame spin-lattice relaxation time measurements Journal of Magnetic Resonance (1969). 24: 411-424. DOI: 10.1016/0022-2364(76)90120-7  0.058
1993 Craig EC, Kuntz ID. Computerized Analysis of 2D NMR Correlation Spectra Using Discrete Matrix Representations Journal of Magnetic Resonance, Series B. 102: 265-284. DOI: 10.1006/jmrb.1993.1096  0.057
1985 Havel TF, Kuntz ID, Crippen B. The theory and practice of distance geometry Bulletin of Mathematical Biology. 47: 157. DOI: 10.1007/BF02459652  0.049
1974 Kollman PA, Kuntz ID. The hydration number of Li+ Journal of the American Chemical Society. 96: 4766-4769.  0.048
1970 Taylor RP, Kuntz ID. Ionic interactions in solution. I. Nuclear magnetic resonance studies Journal of the American Chemical Society. 92: 4813-4823. DOI: 10.1021/Ja00719A009  0.046
1974 Cooke R, Kuntz ID. The properties of water in biological systems Annual Review of Biophysics and Bioengineering. 3: 95-126. PMID 4371481  0.046
1977 Zipp A, Kuntz ID, James TL. Hemoglobin-water interactions in normal and sickle erythrocytes by proton magnetic resonance T1ρ{variant} measurements Archives of Biochemistry and Biophysics. 178: 435-441. PMID 836043 DOI: 10.1016/0003-9861(77)90213-2  0.044
1994 Kuntz ID. Theory and simulation Current Opinion in Structural Biology. 4: 231-233. DOI: 10.1016/S0959-440X(94)90313-1  0.044
1985 Lewis JW, Tilton RF, Einterz CM, Milder SJ, Kuntz ID, Kliger DS. New technique for measuring circular dichroism changes on a nanosecond time scale. Application to (carbonmonoxy)myoglobin and (carbonmonoxy)hemoglobin Journal of Physical Chemistry. 89: 289-294. DOI: 10.1002/Chin.198523051  0.043
2001 Kuntz ID, Case DA. Peter Andrew Kollman. Proteins. 45: 2-3. PMID 11536354 DOI: 10.1002/prot.1117  0.042
1973 Kawai M, Kuntz ID. Optical diffraction studies of muscle fibers Biophysical Journal. 13: 857-876. PMID 4542588  0.041
1961 Kuntz ID, von R. Schleyer P, Allerhand A. Long‐Range N14–H1 Nuclear‐Resonance Coupling in Isonitriles The Journal of Chemical Physics. 35: 1533-1534. DOI: 10.1063/1.1732106  0.037
1966 Hurley WJ, Kuntz ID, Leroi GE. Far-Infrared Studies of Hydrogen Bonding Journal of the American Chemical Society. 88: 3199-3202. DOI: 10.1021/ja00966a004  0.035
1977 Kuntz ID, Zipp A. Water in biological systems New England Journal of Medicine. 297: 262-266. PMID 327320  0.034
1974 Zipp A, Kuntz ID, Rehfeld SJ, Shohet SB. Proton magnetic resonance studies of intracellular water in sickle cells Febs Letters. 43: 9-12. PMID 4212283 DOI: 10.1016/0014-5793(74)81092-6  0.03
1984 Schmidt PG, Kuntz ID. Distance measurements in spin-labeled lysozyme Biochemistry. 23: 4261-4266.  0.021
1969 Taylor RP, Kuntz ID. Nuclear magnetic resonance studies of ion association Journal of the American Chemical Society. 91: 4006-4007. DOI: 10.1021/Ja01042A085  0.019
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