| Year |
Citation |
Score |
| 2009 |
Shortle D. One sequence plus one mutation equals two folds. Proceedings of the National Academy of Sciences of the United States of America. 106: 21011-2. PMID 19996167 DOI: 10.1073/Pnas.0912370107 |
0.441 |
|
| 2007 |
Gebel EB, Shortle D. Characterization of denatured proteins using residual dipolar couplings. Methods in Molecular Biology (Clifton, N.J.). 350: 39-48. PMID 16957316 DOI: 10.1385/1-59745-189-4:39 |
0.631 |
|
| 2006 |
Ohnishi S, Kamikubo H, Onitsuka M, Kataoka M, Shortle D. Conformational preference of polyglycine in solution to elongated structure. Journal of the American Chemical Society. 128: 16338-44. PMID 17165789 DOI: 10.1021/Ja066008B |
0.394 |
|
| 2006 |
Gebel EB, Ruan K, Tolman JR, Shortle D. Multiple alignment tensors from a denatured protein. Journal of the American Chemical Society. 128: 9310-1. PMID 16848448 DOI: 10.1021/Ja0627693 |
0.629 |
|
| 2006 |
Fang Q, Shortle D. Protein refolding in silico with atom-based statistical potentials and conformational search using a simple genetic algorithm. Journal of Molecular Biology. 359: 1456-67. PMID 16678202 DOI: 10.1016/J.Jmb.2006.04.033 |
0.593 |
|
| 2005 |
Fang Q, Shortle D. Enhanced sampling near the native conformation using statistical potentials for local side-chain and backbone interactions. Proteins. 60: 97-102. PMID 15852306 DOI: 10.1002/Prot.20483 |
0.612 |
|
| 2005 |
Fang Q, Shortle D. A consistent set of statistical potentials for quantifying local side-chain and backbone interactions. Proteins. 60: 90-6. PMID 15852305 DOI: 10.1002/Prot.20482 |
0.586 |
|
| 2004 |
Ohnishi S, Lee AL, Edgell MH, Shortle D. Direct demonstration of structural similarity between native and denatured eglin C. Biochemistry. 43: 4064-70. PMID 15065848 DOI: 10.1021/Bi049879B |
0.301 |
|
| 2003 |
Fang Q, Shortle D. Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments. Proteins. 53: 486-90. PMID 14579337 DOI: 10.1002/Prot.10541 |
0.622 |
|
| 2003 |
Ohnishi S, Shortle D. Effects of denaturants and substitutions of hydrophobic residues on backbone dynamics of denatured staphylococcal nuclease. Protein Science : a Publication of the Protein Society. 12: 1530-7. PMID 12824498 DOI: 10.1110/Ps.0306403 |
0.374 |
|
| 2003 |
Shortle D. Propensities, probabilities, and the Boltzmann hypothesis. Protein Science : a Publication of the Protein Society. 12: 1298-302. PMID 12761401 DOI: 10.1110/Ps.0306903 |
0.428 |
|
| 2003 |
Choy WY, Shortle D, Kay LE. Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta. Journal of the American Chemical Society. 125: 1748-58. PMID 12580600 DOI: 10.1021/Ja021179B |
0.407 |
|
| 2003 |
Ohnishi S, Shortle D. Observation of residual dipolar couplings in short peptides. Proteins. 50: 546-51. PMID 12577260 DOI: 10.1002/Prot.10327 |
0.377 |
|
| 2002 |
Ackerman MS, Shortle D. Robustness of the long-range structure in denatured staphylococcal nuclease to changes in amino acid sequence. Biochemistry. 41: 13791-7. PMID 12427042 DOI: 10.1021/Bi020511T |
0.661 |
|
| 2002 |
Shortle D. The expanded denatured state: an ensemble of conformations trapped in a locally encoded topological space. Advances in Protein Chemistry. 62: 1-23. PMID 12418099 DOI: 10.1016/S0065-3233(02)62003-0 |
0.444 |
|
| 2002 |
Ackerman MS, Shortle D. Molecular alignment of denatured states of staphylococcal nuclease with strained polyacrylamide gels and surfactant liquid crystalline phases. Biochemistry. 41: 3089-95. PMID 11863448 DOI: 10.1021/Bi0120796 |
0.604 |
|
| 2002 |
Shortle D. Composites of local structure propensities: evidence for local encoding of long-range structure. Protein Science : a Publication of the Protein Society. 11: 18-26. PMID 11742118 DOI: 10.1110/Ps.Ps.31002 |
0.459 |
|
| 2001 |
Shortle D, Ackerman MS. Persistence of native-like topology in a denatured protein in 8 M urea. Science (New York, N.Y.). 293: 487-9. PMID 11463915 DOI: 10.1126/Science.1060438 |
0.646 |
|
| 2000 |
Shortle D. Prediction of protein structure. Current Biology. 10. PMID 10662677 DOI: 10.1016/S0960-9822(00)00290-6 |
0.355 |
|
| 2000 |
Wrabl JO, Shortle D, Woolf TB. Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: molecular dynamics simulations of native and denatured staphylococcal nuclease. Proteins. 38: 123-33. PMID 10656260 DOI: 10.1002/(Sici)1097-0134(20000201)38:2<123::Aid-Prot2>3.0.Co;2-H |
0.348 |
|
| 1999 |
Sinclair JF, Shortle D. Analysis of long-range interactions in a model denatured state of staphylococcal nuclease based on correlated changes in backbone dynamics Protein Science. 8: 991-1000. PMID 10338010 DOI: 10.1110/Ps.8.5.991 |
0.426 |
|
| 1999 |
Shortle D. Structure prediction: The state of the art Current Biology. 9. PMID 10209093 DOI: 10.1016/S0960-9822(99)80130-4 |
0.312 |
|
| 1999 |
Shortle D. Protein folding as seen from water's perspective Nature Structural Biology. 6: 203-205. PMID 10074933 DOI: 10.1038/6640 |
0.328 |
|
| 1998 |
Shortle D, Simons KT, Baker D. Clustering of low-energy conformations near the native structures of small proteins. Proceedings of the National Academy of Sciences of the United States of America. 95: 11158-62. PMID 9736706 DOI: 10.1073/Pnas.95.19.11158 |
0.305 |
|
| 1997 |
Zhang O, Kay LE, Shortle D, Forman-Kay JD. Comprehensive NOE characterization of a partially folded large fragment of staphylococcal nuclease Δ131Δ, using NMR methods with improved resolution Journal of Molecular Biology. 272: 9-20. PMID 9299333 DOI: 10.1006/Jmbi.1997.1219 |
0.419 |
|
| 1997 |
Mori S, van Zijl PC, Shortle D. Measurement of water-amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique. Proteins. 28: 325-32. PMID 9223179 DOI: 10.1002/(Sici)1097-0134(199707)28:3<325::Aid-Prot3>3.0.Co;2-B |
0.332 |
|
| 1997 |
Shortle D. Structure prediction: Folding proteins by pattern recognition Current Biology. 7. PMID 9162477 DOI: 10.1016/S0960-9822(97)70076-9 |
0.358 |
|
| 1997 |
Gillespie JR, Shortle D. Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures Journal of Molecular Biology. 268: 170-184. PMID 9149150 DOI: 10.1006/Jmbi.1997.0953 |
0.413 |
|
| 1997 |
Gillespie JR, Shortle D. Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels Journal of Molecular Biology. 268: 158-169. PMID 9149149 DOI: 10.1006/Jmbi.1997.0954 |
0.427 |
|
| 1997 |
Wang Y, Shortle D. Residual helical and turn structure in the denatured state of staphylococcal nuclease: Analysis of peptide fragments Folding and Design. 2: 93-100. PMID 9135981 DOI: 10.1016/S1359-0278(97)00013-8 |
0.414 |
|
| 1997 |
Zhang O, Forman-Kay JD, Shortle D, Kay LE. Triple-resonance NOESY-based experiments with improved spectral resolution: Applications to structural characterization of unfolded, partially folded and folded proteins Journal of Biomolecular Nmr. 9: 181-200. PMID 9090132 DOI: 10.1023/A:1018658305040 |
0.366 |
|
| 1996 |
Wrabl JO, Shortle D. Perturbations of the denatured state ensemble: Modeling their effects on protein stability and folding kinetics Protein Science. 5: 2343-2352. PMID 8931153 DOI: 10.1002/Pro.5560051121 |
0.415 |
|
| 1996 |
Wang Y, Shortle D. A dynamic bundle of four adjacent hydrophobic segments in the denatured state of staphylococcal nuclease Protein Science. 5: 1898-1906. PMID 8880914 DOI: 10.1002/Pro.5560050916 |
0.42 |
|
| 1996 |
Shortle D, Wang Y, Gillespie JR, Wrabl JO. Protein folding for realists: A timeless phenomenon Protein Science. 5: 991-1000. PMID 8762131 DOI: 10.1002/Pro.5560050602 |
0.449 |
|
| 1996 |
Shortle DR. Structural analysis of non-native states of proteins by NMR methods Current Opinion in Structural Biology. 6: 24-30. PMID 8696969 DOI: 10.1016/S0959-440X(96)80091-1 |
0.397 |
|
| 1996 |
Meeker AK, Garcia-Moreno E. B, Shortle D. Contributions of the ionizable amino acids to the stability of staphylococcal nuclease Biochemistry. 35: 6443-6449. PMID 8639591 DOI: 10.1021/Bi960171+ |
0.41 |
|
| 1996 |
Shortle D. The denatured state (the other half of the folding equation) and its role in protein stability Faseb Journal. 10: 27-34. PMID 8566543 DOI: 10.1096/Fasebj.10.1.8566543 |
0.434 |
|
| 1995 |
Wang Y, Shortle D. The equilibrium folding pathway of staphylococcal nuclease: Identification of the most stable chain-chain interactions by NMR and CD spectroscopy Biochemistry. 34: 15895-15905. PMID 8519746 DOI: 10.1021/Bi00049A004 |
0.347 |
|
| 1995 |
Shortle D. Staphylococcal nuclease: A showcase of m-value effects Advances in Protein Chemistry. 46: 217-247. PMID 7771319 DOI: 10.1016/S0065-3233(08)60336-8 |
0.396 |
|
| 1995 |
Wang Y, Alexandrescu AT, Shortle D. Initial studies of the equilibrium folding pathway of staphylococcal nuclease. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 348: 27-34. PMID 7770483 DOI: 10.1098/Rstb.1995.0042 |
0.37 |
|
| 1995 |
Shortle D. Protein fold recognition Nature Structural Biology. 2: 91-93. PMID 7749925 DOI: 10.1038/Nsb0295-91 |
0.34 |
|
| 1995 |
Alexandrescu AT, Gittis AG, Abeygunawardana C, Shortle D. NMR structure of a stable "OB-fold" sub-domain isolated from staphylococcal nuclease. Journal of Molecular Biology. 250: 134-43. PMID 7608966 DOI: 10.1006/Jmbi.1995.0365 |
0.345 |
|
| 1995 |
Shortle D, Sondek J. The emerging role of insertions and deletions in protein engineering Current Opinion in Biotechnology. 6: 387-393. PMID 7579648 DOI: 10.1016/0958-1669(95)80067-0 |
0.437 |
|
| 1994 |
Stites WE, Meeker AK, Shortle D. Evidence for strained interactions between side-chains and the polypeptide backbone Journal of Molecular Biology. 235: 27-32. PMID 8289248 DOI: 10.1016/S0022-2836(05)80008-7 |
0.447 |
|
| 1994 |
Alexandrescu AT, Abeygunawardana C, Shortle D. Structure and dynamics of a denatured 131-residue fragment of staphylococcal nuclease: a heteronuclear NMR study. Biochemistry. 33: 1063-72. PMID 8110737 DOI: 10.1021/Bi00171A004 |
0.462 |
|
| 1994 |
Creighton TE, Shortle D. Electrophoretic characterization of the denatured states of staphylococcal nuclease. Journal of Molecular Biology. 242: 670-82. PMID 7932723 DOI: 10.1006/Jmbi.1994.1616 |
0.412 |
|
| 1994 |
Alexandrescu AT, Shortle D. Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease. Journal of Molecular Biology. 242: 527-46. PMID 7932708 DOI: 10.1006/Jmbi.1994.1598 |
0.362 |
|
| 1993 |
Keefe LJ, Sondek J, Shortle D, Lattman EE. The α aneurism: A structural motif revealed in an insertion mutant of staphylococcal nuclease Proceedings of the National Academy of Sciences of the United States of America. 90: 3275-3279. PMID 8475069 DOI: 10.1073/Pnas.90.8.3275 |
0.36 |
|
| 1993 |
Green SM, Shortle D. Patterns of nonadditivity between pairs of stability mutations in staphylococcal nuclease Biochemistry. 32: 10131-10139. PMID 8399139 DOI: 10.1021/Bi00089A032 |
0.453 |
|
| 1993 |
Shortle D, Abeygunawardana C. NMR analysis of the residual structure in the denatured state of an unusual mutant of staphylococcal nuclease Structure. 1: 121-134. PMID 8069625 DOI: 10.1016/0969-2126(93)90027-E |
0.456 |
|
| 1993 |
Shortle D. Denatured states of proteins and their roles in folding and stability Current Opinion in Structural Biology. 3: 66-74. DOI: 10.1016/0959-440X(93)90204-X |
0.415 |
|
| 1992 |
Flanagan JM, Kataoka M, Shortle D, Engelman DM. Truncated staphylococcal nuclease is compact but disordered Proceedings of the National Academy of Sciences of the United States of America. 89: 748-752. PMID 1731350 DOI: 10.1073/Pnas.89.2.748 |
0.417 |
|
| 1992 |
Sondek J, Shortle D. Structural and energetic differences between insertions and substitutions in staphylococcal nuclease Proteins: Structure, Function and Genetics. 13: 132-140. PMID 1620695 DOI: 10.1002/Prot.340130206 |
0.455 |
|
| 1992 |
Green SM, Meeker AK, Shortle D. Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: Evidence for mutational effects on the free energy of the denatured state Biochemistry. 31: 5717-5728. PMID 1610820 DOI: 10.1021/Bi00140A005 |
0.442 |
|
| 1992 |
Sondek J, Shortle D. A general strategy for random insertion and substitution mutagenesis: Substoichiometric coupling of trinucleotide phosphoramidites Proceedings of the National Academy of Sciences of the United States of America. 89: 3581-3585. PMID 1565654 DOI: 10.1073/Pnas.89.8.3581 |
0.407 |
|
| 1992 |
Shortle D. Mutational studies of protein structures and their stabilities Quarterly Reviews of Biophysics. 25: 205-250. PMID 1518925 DOI: 10.1017/S0033583500004674 |
0.424 |
|
| 1992 |
Shortle D, Hue Sun Chan, Dill KA. Modeling the effects of mutations on the denatured states of proteins Protein Science. 1: 201-215. PMID 1304903 DOI: 10.1002/Pro.5560010202 |
0.367 |
|
| 1991 |
Stites WE, Gittis AG, Lattman EE, Shortle D. In a staphylococcal nuclease mutant the side-chain of a lysine replacing valine 66 is fully buried in the hydrophobic core. Journal of Molecular Biology. 221: 7-14. PMID 1920420 DOI: 10.1016/0022-2836(91)80195-Z |
0.328 |
|
| 1991 |
Dill KA, Shortle D. Denatured states of proteins. Annual Review of Biochemistry. 60: 795-825. PMID 1883209 DOI: 10.1146/Annurev.Bi.60.070191.004051 |
0.434 |
|
| 1990 |
Sondek J, Shortle D. Accomodation of single amino acid insertions by the native state of staphylococcal nuclease Proteins: Structure, Function and Genetics. 7: 299-305. PMID 2381904 DOI: 10.1002/Prot.340070402 |
0.333 |
|
| 1990 |
Shortle D, Stites WE, Meeker AK. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease Biochemistry. 29: 8033-8041. PMID 2261461 DOI: 10.1021/Bi00487A007 |
0.46 |
|
| 1990 |
Dunn TM, Shortle D. Null alleles of SAC7 suppress temperature-sensitive actin mutations in Saccharomyces cerevisiae. Molecular and Cellular Biology. 10: 2308-14. PMID 2183030 DOI: 10.1128/Mcb.10.5.2308 |
0.326 |
|
| 1990 |
Weber DJ, Serpersu EH, Shortle D, Mildvan AS. Diverse interactions between the individual mutations in a double mutant at the active site of staphylococcal nuclease. Biochemistry. 29: 8632-42. PMID 1702994 DOI: 10.1021/Bi00489A020 |
0.38 |
|
| 1989 |
Kuliopulos A, Mildvan AS, Shortle D, Talalay P. Kinetic and ultraviolet spectroscopic studies of active-site mutants of delta 5-3-ketosteroid isomerase. Biochemistry. 28: 149-59. PMID 2706241 DOI: 10.1021/Bi00427A022 |
0.383 |
|
| 1989 |
Shortle D, Meeker AK, Gerring SL. Effects of denaturants at low concentrations on the reversible denaturation of staphylococcal nuclease Archives of Biochemistry and Biophysics. 272: 103-113. PMID 2544138 DOI: 10.1016/0003-9861(89)90200-2 |
0.336 |
|
| 1989 |
Shortle D, Meeker AK. Residual structure in large fragments of staphylococcal nuclease: Effects of amino acid substitutions Biochemistry. 28: 936-944. PMID 2540825 DOI: 10.1021/Bi00429A003 |
0.466 |
|
| 1988 |
Shortle D, Meeker AK, Freire E. Stability mutants of staphylococcal nuclease: Large compensating enthalpy-entropy changes for the reversible denaturation reaction Biochemistry. 27: 4761-4768. PMID 3167015 DOI: 10.1021/Bi00413A027 |
0.356 |
|
| 1987 |
Serpersu EH, Shortle D, Mildvan AS. Kinetic and magnetic resonance studies of active-site mutants of staphylococcal nuclease: factors contributing to catalysis. Biochemistry. 26: 1289-300. PMID 3567171 DOI: 10.1021/Bi00379A014 |
0.363 |
|
| 1987 |
Kuliopulos A, Shortle D, Talalay P. Isolation and sequencing of the gene encoding delta 5-3-ketosteroid isomerase of Pseudomonas testosteroni: overexpression of the protein Proceedings of the National Academy of Sciences of the United States of America. 84: 8893-8897. PMID 3480517 DOI: 10.1073/Pnas.84.24.8893 |
0.386 |
|
| 1986 |
Shortle D. Guanidine hydrochloride denaturation studies of mutant forms of staphylococcal nuclease Journal of Cellular Biochemistry. 30: 281-289. PMID 3519625 DOI: 10.1002/Jcb.240300402 |
0.42 |
|
| 1986 |
Serpersu EH, Shortle D, Mildvan AS. Kinetic and magnetic resonance studies of effects of genetic substitution of a Ca2+-liganding amino acid in staphylococcal nuclease. Biochemistry. 25: 68-77. PMID 3513826 DOI: 10.1021/Bi00349A011 |
0.346 |
|
| 1986 |
Shortle D, Meeker AK. Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation Proteins: Structure, Function and Genetics. 1: 81-89. PMID 3449854 DOI: 10.1002/Prot.340010113 |
0.391 |
|
| 1985 |
Botstein D, Shortle D. Strategies and applications of in vitro mutagenesis Science. 229: 1193-1201. PMID 2994214 DOI: 10.1126/Science.2994214 |
0.461 |
|
| 1984 |
Shortle D, Novick P, Botstein D. Construction and genetic characterization of temperature-sensitive mutant alleles of the yeast actin gene Proceedings of the National Academy of Sciences of the United States of America. 81: 4889-4893. PMID 6379652 DOI: 10.1073/Pnas.81.15.4889 |
0.653 |
|
| 1983 |
Shortle D, Botstein D. Directed mutagenesis with sodium bisulfite Methods in Enzymology. 457-468. PMID 6312263 DOI: 10.1016/0076-6879(83)00073-7 |
0.573 |
|
| 1983 |
Shortle D. A genetic system for analysis of staphylococcal nuclease Gene. 22: 181-189. PMID 6307819 DOI: 10.1016/0378-1119(83)90102-6 |
0.331 |
|
| 1982 |
Shortle D, Haber JE, Botstein D. Lethal disruption of the yeast actin gene by integrative DNA transformation Science. 217: 371-373. PMID 7046050 DOI: 10.1126/Science.7046050 |
0.467 |
|
| 1982 |
Shortle D, Grisafi P, Benkovic SJ, Botstein D. Gap misrepair mutagenesis: Efficient site-directed induction of transition, transversion, and frameshift mutations in vitro Proceedings of the National Academy of Sciences of the United States of America. 79: 1588-1592. PMID 7041125 DOI: 10.1073/Pnas.79.5.1588 |
0.56 |
|
| 1982 |
Shortle D, Botstein D. Single-stranded gaps as localized targets for in vitro mutagenesis Basic Life Sciences. 20: 147-155. PMID 6287991 DOI: 10.1007/978-1-4613-3476-7_8 |
0.518 |
|
| 1981 |
Shortle D, DiMaio D, Nathans D. Directed mutagenesis. Annual Review of Genetics. 15: 265-94. PMID 6279018 DOI: 10.1146/annurev.ge.15.120181.001405 |
0.634 |
|
| 1980 |
Shortle D, Koshland D, Weinstock GM, Botstein D. Segment-directed mutagenesis: Construction in vitro of point mutations limited to a small predetermined region of a circular DNA molecule Proceedings of the National Academy of Sciences of the United States of America. 77: 5375-5379. PMID 6254078 DOI: 10.1073/Pnas.77.9.5375 |
0.716 |
|
| 1979 |
Shortle DR, Margolskee RF, Nathans D. Mutational analysis of the simian virus 40 replicon: pseudorevertants of mutants with a defective replication origin. Proceedings of the National Academy of Sciences of the United States of America. 76: 6128-31. PMID 230499 DOI: 10.1073/Pnas.76.12.6128 |
0.692 |
|
| 1979 |
Shortle D, Nathans D. Regulatory mutants of simian virus 40: constructed mutants with base substitutions at the origin of DNA replication. Journal of Molecular Biology. 131: 801-17. PMID 229233 DOI: 10.1016/0022-2836(79)90202-X |
0.627 |
|
| 1979 |
Shortle D, Nathans D. Mutants of simian virus 40 with base substitutions at the origin of DNA replication. Cold Spring Harbor Symposia On Quantitative Biology. 43: 663-8. PMID 226311 DOI: 10.1101/Sqb.1979.043.01.074 |
0.57 |
|
| 1978 |
Shortle D, Nathans D. Local mutagenesis: a method for generating viral mutants with base substitutions in preselected regions of the viral genome. Proceedings of the National Academy of Sciences of the United States of America. 75: 2170-4. PMID 209457 DOI: 10.1073/Pnas.75.5.2170 |
0.628 |
|
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