| Year |
Citation |
Score |
| 2018 |
Joyce AP, Havranek JJ. Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors. Quantitative Biology (Beijing, China). 6: 68-84. PMID 37990674 DOI: 10.1007/s40484-018-0130-0 |
0.32 |
|
| 2018 |
Bodmer NK, Havranek JJ. Efficient minimization of multipole electrostatic potentials in torsion space. Plos One. 13: e0195578. PMID 29641557 DOI: 10.1371/Journal.Pone.0195578 |
0.37 |
|
| 2016 |
Chang YK, Srivastava Y, Hu C, Joyce A, Yang X, Zuo Z, Havranek JJ, Stormo GD, Jauch R. Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq. Nucleic Acids Research. PMID 27915232 DOI: 10.1093/Nar/Gkw1198 |
0.309 |
|
| 2015 |
Zhang C, Myers CA, Qi Z, Mitra RD, Corbo JC, Havranek JJ. Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex. Nucleic Acids Research. 43: 9076-85. PMID 26365240 DOI: 10.1093/Nar/Gkv901 |
0.416 |
|
| 2015 |
Joyce AP, Zhang C, Bradley P, Havranek JJ. Structure-based modeling of protein: DNA specificity. Briefings in Functional Genomics. 14: 39-49. PMID 25414269 DOI: 10.1093/Bfgp/Elu044 |
0.458 |
|
| 2015 |
Borgo B, Havranek JJ. Computer-aided design of a catalyst for Edman degradation utilizing substrate-assisted catalysis Protein Science. 24: 571-579. DOI: 10.1002/Pro.2633 |
0.367 |
|
| 2014 |
Borgo B, Havranek JJ. Motif-directed redesign of enzyme specificity. Protein Science : a Publication of the Protein Society. 23: 312-20. PMID 24407908 DOI: 10.1002/Pro.2417 |
0.484 |
|
| 2013 |
Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). Plos One. 8: e63906. PMID 23717507 DOI: 10.1371/Journal.Pone.0063906 |
0.362 |
|
| 2013 |
Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, et al. Scientific benchmarks for guiding macromolecular energy function improvement. Methods in Enzymology. 523: 109-43. PMID 23422428 DOI: 10.1016/B978-0-12-394292-0.00006-0 |
0.327 |
|
| 2012 |
Borgo B, Havranek JJ. Automated selection of stabilizing mutations in designed and natural proteins. Proceedings of the National Academy of Sciences of the United States of America. 109: 1494-9. PMID 22307603 DOI: 10.1073/Pnas.1115172109 |
0.511 |
|
| 2010 |
Havranek JJ. Specificity in computational protein design. The Journal of Biological Chemistry. 285: 31095-9. PMID 20670934 DOI: 10.1074/Jbc.R110.157685 |
0.549 |
|
| 2010 |
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins. 78: 3212-8. PMID 20597089 DOI: 10.1002/Prot.22784 |
0.367 |
|
| 2010 |
Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Research. 38: 5601-8. PMID 20435674 DOI: 10.1093/Nar/Gkq283 |
0.461 |
|
| 2009 |
Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D. Exploitation of binding energy for catalysis and design. Nature. 461: 1300-4. PMID 19865174 DOI: 10.1038/Nature08508 |
0.403 |
|
| 2009 |
Havranek JJ, Baker D. Motif-directed flexible backbone design of functional interactions. Protein Science : a Publication of the Protein Society. 18: 1293-305. PMID 19472357 DOI: 10.1002/Pro.142 |
0.552 |
|
| 2009 |
Muratore KE, Seeliger MA, Wang Z, Fomina D, Neiswinger J, Havranek JJ, Baker D, Kuriyan J, Cole PA. Comparative analysis of mutant tyrosine kinase chemical rescue. Biochemistry. 48: 3378-86. PMID 19260709 DOI: 10.1021/Bi900057G |
0.341 |
|
| 2007 |
Stankunas K, Bayle JH, Havranek JJ, Wandless TJ, Baker D, Crabtree GR, Gestwicki JE. Rescue of degradation-prone mutants of the FK506-rapamycin binding (FRB) protein with chemical ligands. Chembiochem : a European Journal of Chemical Biology. 8: 1162-9. PMID 17525916 DOI: 10.1002/Cbic.200700087 |
0.388 |
|
| 2007 |
Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker D. High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. Journal of Molecular Biology. 366: 1209-21. PMID 17196978 DOI: 10.1016/J.Jmb.2006.11.080 |
0.506 |
|
| 2006 |
Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 441: 656-9. PMID 16738662 DOI: 10.1038/Nature04818 |
0.453 |
|
| 2005 |
Morozov AV, Havranek JJ, Baker D, Siggia ED. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Research. 33: 5781-98. PMID 16246914 DOI: 10.1093/Nar/Gki875 |
0.49 |
|
| 2004 |
Havranek JJ, Duarte CM, Baker D. A simple physical model for the prediction and design of protein-DNA interactions. Journal of Molecular Biology. 344: 59-70. PMID 15504402 DOI: 10.1016/J.Jmb.2004.09.029 |
0.515 |
|
| 2003 |
Havranek JJ, Harbury PB. Automated design of specificity in molecular recognition. Nature Structural Biology. 10: 45-52. PMID 12459719 DOI: 10.1038/Nsb877 |
0.617 |
|
| 1999 |
Havranek JJ, Harbury PB. Tanford-Kirkwood electrostatics for protein modeling. Proceedings of the National Academy of Sciences of the United States of America. 96: 11145-50. PMID 10500144 DOI: 10.1073/Pnas.96.20.11145 |
0.607 |
|
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