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Blind ab initio structure prediction of CASP3 targets
Simons, K.T., Bonneau, et al. Proteins 3, 171-176 (1999) To generate structures consistent with both the local and non-local interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons, K.T.…
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Experiment and theory highlight role of native state topology in SH3 folding
Riddle, D.S., Grantcharova, V.P., et al. Nat Struct Biol 6, 1016-1204. (1999) We use a combination of experiments, computer simulations and simple model calculations to characterize, first, the folding transition state ensemble of the src SH3 domain, and second, the features of the protein that determine its folding mechanism. Kinetic analysis of mutations at 52…
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A correlation between folding rate and contact order
Plaxco, K. W., Simons, K. T. et al. J. Mol. Biol. 277, 985-994. (1998) Our studies have revealed a significant correlation between the average sequence seqaration between contacting residues in the native state (contact order) and the folding rate of simple, single domain proteins. Calculate the contact order for your protein or a protein in…
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The I-sites library of sequence-structure motifs
Bystroff, C. and Baker, D. J. Mol. Biol. 281, 565-77. (1998) I-Sites Library Homepage I-Sites Prediction Server I-Sites clusters by motif
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Sequences of small proteins are not optimized for rapid folding
Kim, D. E., Gu, H., and Baker, D. Proc. Natl. Acad. Sci, 95, 4982-4986 (1998) Distributions of free energies of unfolding and refolding rates in randomized protein L variants compared to wild type.
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A folded, functional SH3 domain built largely from a five letter amino acid alphabet
Riddle, D., Santiago, J., et al. Nature Structural Biology 4, 805-809. (1997) Diagram showing the positions of simplified residues (I, K, E, A, G) in red for FP2 in the wild type SH3 structure. Side chains of residues involved in ligand binding are displayed and residues where simplification was not attempted are in light blue. The…