Research Topics
Species | James J HavranekSummaryAffiliation: Washington University School of Medicine Country: USA Publications
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Detail Information
Publications
Motif-directed flexible backbone design of functional interactionsJames J Havranek
Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
Protein Sci 18:1293-305. 2009..We compare the efficiency of this method with the alternative approach of building and screening alternate backbone conformations...- Specificity in computational protein designJames J Havranek
Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
J Biol Chem 285:31095-9. 2010..Although specificity may, in some cases, be achieved by optimization of a desired protein in isolation, methods have been developed to address directly the desire for proteins that exhibit specific functions and interactions... - Exploitation of binding energy for catalysis and designSummer B Thyme
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Nature 461:1300-4. 2009..Our results illustrate how classical enzymology and modern protein design can each inform the other... - Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairsJustin Ashworth
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Nucleic Acids Res 38:5601-8. 2010.... - Computational redesign of endonuclease DNA binding and cleavage specificityJustin Ashworth
Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Nature 441:656-9. 2006..These results suggest that computational protein design methods can have an important role in the creation of novel highly specific endonucleases for gene therapy and other applications... - High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein designGautam Dantas
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 366:1209-21. 2007.... - Rosetta in CAPRI rounds 13-19Sarel J Fleishman
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 78:3212-8. 2010..Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement... - A simple physical model for the prediction and design of protein-DNA interactionsJames J Havranek
Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 344:59-70. 2004..When combined with algorithms that optimize specificity directly, the simple computational model developed here should be useful for the engineering of proteins with novel DNA-binding specificities... - Automated selection of stabilizing mutations in designed and natural proteinsBenjamin Borgo
Program in Computational and Systems Biology, Washington University in St Louis, St Louis, MO 63110, USA
Proc Natl Acad Sci U S A 109:1494-9. 2012..We believe our method will be a valuable tool for both improving upon designed proteins and conferring increased stability upon native proteins... - ROSETTA3: an object-oriented software suite for the simulation and design of macromoleculesAndrew Leaver-Fay
Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, USA
Methods Enzymol 487:545-74. 2011..This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform...