RECENT PUBLICATIONS:
Gebel, E. Ruan, K.; Tolman, J.R and Shortle, D. (2006) Multiple alignment tensors from a denatured protein. J. Am. Chem. Soc. Proteins 60:97-102.
Gebel, E. and Shortle, D (2006) Characterization of denatured proteins using residual dipolar couplings. Methods in Molecular Biology, in press.
Fang, Q and Shortle, D (2006) Protein refolding in silico with atom-based statistical potentials and conformational search using a simple genetic algorithm. J. Mol. Biol. 359:1456-1467.
Fang Q. and Shortle, D. (2005) A consistent set of statistical potentials for quantifying local side-chain and backbone interactions. Proteins 60: 90-96.
Fang, Q. and Shortle, D. (2005) Enhanced sampling near the native conformation using statistical potentials for local side-chain and backbone interactions. Proteins. 60: 97-102.
Ohnishi, S., Lee, A.L., Edgell, M.H. and Shortle, D. (2004) Direct demonstration of structural similarity between native and denatured eglin C. Biochemistry 43: 4064-4070.
Ohnishi, S. and Shortle, D. (2003) Observation of residual dipolar couplings in short peptides. Proteins: 50: 546-51
Choy, W.-Y., Shortle, D. and Kay, L.E. (2003) Side chain dynamics in unfolded protein states: A 2H spin relaxation study of D131D. J. Amer. Chem. Soc., 125:1748-1758.
Fang, Q. and Shortle, D (2003) Prediction of Protein Structure by Emphasizing Local Side-Chain / Backbone Interactions in Ensembles of Turn Fragments. Proteins: 53: 486-490.
Shortle, D. (2003) Propensities, probabilities, and the Boltzmann hypothesis. Protein Science 12: 1298-1302.
Ohnishi S. and Shortle, D. (2003) Effect of denaturants and substitutions of hydrophobic residues on backbone dynamics of denatured staphylococcal nuclease. Protein Science 12: 1530-1537.
Shortle, D. (2002) Composites of Local Structural Propensities: Evidence for Local Encoding of Long Range Structure. Protein Science 11: 18-26.
Ackerman, M. S. and Shortle, D. (2002) Molecular Alignment of Denatured States of Staphylococcal Nuclease with Strained Polyacrylamide Gels and Alkyl-PEG Bicelles. Biochemistry 41: 3089-3095.
Ackerman, M. S. and Shortle, D. (2002) Robustness of the long-range structure in denatured staphylococcal nuclease to changes in sequence. Biochemistry 41: 13791-13797.
Shortle, D. (2002) The Expanded Denatured State: An Ensemble of Conformations Trapped in a Locally Encoded Topological Space. Adv. Protein Chem. 62: 1-23.
Shortle, D. and Ackerman, M. S. (2001) Persistence of native-like topology in a denatured protein in 8 M urea. Science 293: 487-489.
Shortle, D. (2000) Prediction of protein structure (a primer). Current Biol. 10: R49-R51.