J. Havranek

发表

Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

Brian D. Weitzner, Jeffrey J. Gray, Bryan S. Der, 2013, PloS one.

High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design

D. Baker, B. Kuhlman, G. Dantas, 2007, Journal of molecular biology.

Structure-based modeling of protein: DNA specificity.

Adam P. Joyce, P. Bradley, J. Havranek, 2015, Briefings in functional genomics.

A simple physical model for the prediction and design of protein-DNA interactions.

D. Baker, J. Havranek, C. M. Duarte, 2004, Journal of molecular biology.

Protein–DNA binding specificity predictions with structural models

D. Baker, E. Siggia, A. Morozov, 2005, Nucleic acids research.

Inhibition of Bacterial Virulence: Drug-Like Molecules Targeting the Salmonella enterica PhoP Response Regulator

James J Havranek, Garland R Marshall, Yat T. Tang, 2012, Chemical biology & drug design.

Exploitation of binding energy for catalysis and design

Summer B. Thyme, D. Baker, B. Stoddard, 2009, Nature.

Automated design of specificity in molecular recognition

P. Harbury, J. Havranek, 2003, Nature Structural Biology.

Computational redesign of endonuclease DNA binding and cleavage specificity

D. Baker, B. Stoddard, R. Monnat, 2006, Nature.

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

David Baker, Barry L. Stoddard, Justin Ashworth, 2010, Nucleic acids research.

Rescue of Degradation‐Prone Mutants of the FK506‐Rapamycin Binding (FRB) Protein with Chemical Ligands

K. Stankunas, G. Crabtree, T. Wandless, 2007, Chembiochem : a European journal of chemical biology.

Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq

Adam P. Joyce, G. Stormo, J. Havranek, 2016, Nucleic acids research.

Efficient minimization of multipole electrostatic potentials in torsion space

J. Havranek, Nicholas K Bodmer, 2018, PloS one.

Tanford-Kirkwood electrostatics for protein modeling.

P. Harbury, J. Havranek, P B Harbury, 1999, Proceedings of the National Academy of Sciences of the United States of America.

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

Jens Meiler, Florian Richter, David Baker, 2011, Methods in enzymology.

Comparative analysis of mutant tyrosine kinase chemical rescue.

D. Baker, J. Kuriyan, J. Havranek, 2009, Biochemistry.

Scientific benchmarks for guiding macromolecular energy function improvement.

Jack Snoeyink, Yifan Song, James Thompson, 2013, Methods in enzymology.

Redesign of the monomer–monomer interface of Cre recombinase yields an obligate heterotetrameric complex

R. Mitra, J. Corbo, C. Myers, 2015, Nucleic acids research.

Characterization of Leber Congenital Amaurosis-associated NMNAT1 Mutants*

J. Milbrandt, Benjamin Borgo, J. Havranek, 2015, The Journal of Biological Chemistry.

Characterization of LCA 9-associated NMNAT 1 mutants Characterization of Leber ’ s Congenital Amaurosis-associated NMNAT 1 Mutants

J. Milbrandt, Benjamin Borgo, J. Havranek, 2015 .

Automated selection of stabilizing mutations in designed and natural proteins

James J Havranek, Benjamin Borgo, J. Havranek, 2012, Proceedings of the National Academy of Sciences.

Motif‐directed flexible backbone design of functional interactions

David Baker, James J Havranek, D. Baker, 2009, Protein science : a publication of the Protein Society.

Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors

Adam P. Joyce, James J. Havranek, J. Havranek, 2018, Quantitative Biology.

Caenorhabditis elegans glp-4 Encodes a Valyl Aminoacyl tRNA Synthetase

E. Mardis, Y. Kohara, Paul M. Fox, 2015, G3: Genes, Genomes, Genetics.

Rosetta in CAPRI rounds 13–19

David Baker, Sarel J Fleishman, Rhiju Das, 2010, Proteins.

Motif-directed redesign of enzyme specificity

James J Havranek, Benjamin Borgo, J. Havranek, 2014, Protein science : a publication of the Protein Society.

Computational redesign of endonuclease DNA binding and cleavage specificity

Ashworth, B. Stoddard, R. Monnat, 2006 .

Relation Between Obesity and Blunted Striatal Response to Food Is Moderated by TaqIA A1 Allele

J. Michael Schurr, V. Zhurkin, E. Siggia, 2008, Science.

Computational redesign of endonuclease DNA binding and cleavage specificity

B. Stoddard, R. Monnat, J. Havranek, 2006, Nature.

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

Oliver F. Lange, Jeffrey J. Gray, Ian W. Davis, 2011, Methods in enzymology.

Structure-based modeling of protein: DNA specificity.

Adam P. Joyce, P. Bradley, J. Havranek, 2015, Briefings in functional genomics.

Computer-aided design of a catalyst for Edman degradation utilizing substrate-assisted catalysis

Benjamin Borgo, J. Havranek, 2014, Protein Science : A Publication of the Protein Society.

Specificity in Computational Protein Design*

James J. Havranek, J. Havranek, 2010, The Journal of Biological Chemistry.

Relation Between Obesity and Blunted Striatal Response to Food Is Moderated by TaqIA A1 Allele

J. Michael Schurr, V. Zhurkin, E. Siggia, 2008, Science.

Protein–DNA binding specificity predictions with structural models

E. Siggia, A. Morozov, J. Havranek, 2005, Nucleic acids research.