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Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.. Proceedings of the National Academy of Sciences of the United States of America. 110(39), 15674-9.(2013).
Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. Journal of molecular biology. 379(4), 745-59.(2008).
Evaluation and optimization of discrete state models of protein folding.. The journal of physical chemistry. B. 116(37), 11405-13.(2012).
Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature chemical biology.(2012).
Algorithm discovery by protein folding game players.. Proceedings of the National Academy of Sciences of the United States of America.(2011).
Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature structural & molecular biology. 18(10), 1175-7.(2011).
Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution. Journal of molecular biology. 407(3), 391-412.(2011).
Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.. Proceedings of the National Academy of Sciences of the United States of America. 109(26), 10358-63.(2012).
Computation of conformational coupling in allosteric proteins. PLoS computational biology. 5(8), e1000484.(2009).
Sampling bottlenecks in de novo protein structure prediction. Journal of molecular biology. 393(1), 249-60.(2009).
A breakdown of symmetry in the folding transition state of protein L. Journal of molecular biology. 298(5), 971-84.(2000).
Protein structure prediction and analysis using the Robetta server. Nucleic acids research. 32(Web Server issue), W526-31.(2004).
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins. 61 Suppl 7, 193-200.(2005).
Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase. Acta crystallographica. Section D. 57(Pt 5), 759-62.(2001).
The single helix in protein L is largely disrupted at the rate-limiting step in folding. Journal of molecular biology. 284(3), 807-15.(1998).
The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proceedings of the National Academy of Sciences of the United States of America. 95(9), 4982-6.(1998).
Computational enzyme design. Angewandte Chemie (International ed. in English). 52(22), 5700-25.(2013).
Evaluation and ranking of enzyme designs. Protein science. 19(9), 1760-73.(2010).
Conservation, variability and the modeling of active protein kinases. PloS one. 2(10), e982.(2007).
Principles for designing ideal protein structures.. Nature. 491(7423), 222-7.(2012).
Computational thermostabilization of an enzyme. Science. 308(5723), 857-60.(2005).
Computational design of protein-protein interactions. Current opinion in chemical biology. 8(1), 91-7.(2004).
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. Journal of molecular biology. 326(4), 1239-59.(2003).
Computational alanine scanning of protein-protein interfaces. Science's STKE. 2004(219), pl2.(2004).
A simple physical model for binding energy hot spots in protein-protein complexes. Proceedings of the National Academy of Sciences of the United States of America. 99(22), 14116-21.(2002).
Computational redesign of protein-protein interaction specificity. Nature structural & molecular biology. 11(4), 371-9.(2004).
Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nature structural biology. 9(6), 458-63.(2002).
Accurate computer-based design of a new backbone conformation in the second turn of protein L. Journal of molecular biology. 315(3), 471-7.(2002).
Conversion of monomeric protein L to an obligate dimer by computational protein design. Proceedings of the National Academy of Sciences of the United States of America. 98(19), 10687-91.(2001).
Native protein sequences are close to optimal for their structures. Proceedings of the National Academy of Sciences of the United States of America. 97(19), 10383-8.(2000).
Design of a novel globular protein fold with atomic-level accuracy. Science. 302(5649), 1364-8.(2003).
Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins. 54(2), 282-8.(2004).