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Items: 1 to 50 of 81

1.

Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation.

Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas JE, Heinonen M, Kortemme T.

J Phys Chem B. 2018 Feb 15. doi: 10.1021/acs.jpcb.7b11367. [Epub ahead of print]

PMID:
29401388
2.

Engineering a light-activated caspase-3 for precise ablation of neurons in vivo.

Smart AD, Pache RA, Thomsen ND, Kortemme T, Davis GW, Wells JA.

Proc Natl Acad Sci U S A. 2017 Sep 26;114(39):E8174-E8183. doi: 10.1073/pnas.1705064114. Epub 2017 Sep 11.

PMID:
28893998
3.

Deconstruction of the Ras switching cycle through saturation mutagenesis.

Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J.

Elife. 2017 Jul 7;6. pii: e27810. doi: 10.7554/eLife.27810.

4.

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL Jr, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ.

J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048. doi: 10.1021/acs.jctc.7b00125. Epub 2017 May 12.

PMID:
28430426
5.

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting.

Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo EC, See SK, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS.

Elife. 2016 Apr 25;5. pii: e15802. doi: 10.7554/eLife.15802.

6.

Design of Light-Controlled Protein Conformations and Functions.

Ritterson RS, Hoersch D, Barlow KA, Kortemme T.

Methods Mol Biol. 2016;1414:197-211. doi: 10.1007/978-1-4939-3569-7_12.

7.

A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine.

Hoersch D, Kortemme T.

Structure. 2016 Apr 5;24(4):576-584. doi: 10.1016/j.str.2016.02.015. Epub 2016 Mar 24.

8.

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

Ollikainen N, de Jong RM, Kortemme T.

PLoS Comput Biol. 2015 Sep 23;11(9):e1004335. doi: 10.1371/journal.pcbi.1004335. eCollection 2015.

9.

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

Ó Conchúir S, Barlow KA, Pache RA, Ollikainen N, Kundert K, O'Meara MJ, Smith CA, Kortemme T.

PLoS One. 2015 Sep 3;10(9):e0130433. doi: 10.1371/journal.pone.0130433. eCollection 2015.

10.

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.

O'Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B.

J Chem Theory Comput. 2015 Feb 10;11(2):609-22. doi: 10.1021/ct500864r.

11.

Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.

Melero C, Ollikainen N, Harwood I, Karpiak J, Kortemme T.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15426-31. doi: 10.1073/pnas.1410624111. Epub 2014 Oct 13.

12.

Editorial overview: Engineering and design: raising the bar through innovation and integration.

Koide S, Kortemme T.

Curr Opin Struct Biol. 2014 Aug;27:vi-viii. doi: 10.1016/j.sbi.2014.08.004. Epub 2014 Aug 28. No abstract available.

PMID:
25175941
13.

Reprogramming an ATP-driven protein machine into a light-gated nanocage.

Hoersch D, Roh SH, Chiu W, Kortemme T.

Nat Nanotechnol. 2013 Dec;8(12):928-32. doi: 10.1038/nnano.2013.242. Epub 2013 Nov 24.

14.

Amino-acid site variability among natural and designed proteins.

Jackson EL, Ollikainen N, Covert AW 3rd, Kortemme T, Wilke CO.

PeerJ. 2013 Nov 12;1:e211. doi: 10.7717/peerj.211. eCollection 2013.

15.

Computational protein design quantifies structural constraints on amino acid covariation.

Ollikainen N, Kortemme T.

PLoS Comput Biol. 2013;9(11):e1003313. doi: 10.1371/journal.pcbi.1003313. Epub 2013 Nov 14.

16.

Design of a photoswitchable cadherin.

Ritterson RS, Kuchenbecker KM, Michalik M, Kortemme T.

J Am Chem Soc. 2013 Aug 28;135(34):12516-9. doi: 10.1021/ja404992r. Epub 2013 Aug 14.

17.

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).

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, Gray JJ, Das R.

PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013.

18.

Improvements to robotics-inspired conformational sampling in rosetta.

Stein A, Kortemme T.

PLoS One. 2013 May 21;8(5):e63090. doi: 10.1371/journal.pone.0063090. Print 2013.

19.

Scientific benchmarks for guiding macromolecular energy function improvement.

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, Baker D, Kuhlman B.

Methods Enzymol. 2013;523:109-43. doi: 10.1016/B978-0-12-394292-0.00006-0.

20.

Flexible backbone sampling methods to model and design protein alternative conformations.

Ollikainen N, Smith CA, Fraser JS, Kortemme T.

Methods Enzymol. 2013;523:61-85. doi: 10.1016/B978-0-12-394292-0.00004-7.

21.

Design of a phosphorylatable PDZ domain with peptide-specific affinity changes.

Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJS, Jacobson MP, Kortemme T.

Structure. 2013 Jan 8;21(1):54-64. doi: 10.1016/j.str.2012.10.007. Epub 2012 Nov 15.

22.

In support of the BMRB.

Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S.

Nat Struct Mol Biol. 2012 Sep;19(9):854-60. doi: 10.1038/nsmb.2371. No abstract available.

PMID:
22955930
23.

Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design.

Humphris-Narayanan E, Akiva E, Varela R, Ó Conchúir S, Kortemme T.

PLoS Comput Biol. 2012;8(8):e1002639. doi: 10.1371/journal.pcbi.1002639. Epub 2012 Aug 23.

24.

Cost-benefit tradeoffs in engineered lac operons.

Eames M, Kortemme T.

Science. 2012 May 18;336(6083):911-5. doi: 10.1126/science.1219083.

25.

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.

Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5277-82. doi: 10.1073/pnas.1114487109. Epub 2012 Mar 7.

26.

Global landscape of HIV-human protein complexes.

Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ.

Nature. 2011 Dec 21;481(7381):365-70. doi: 10.1038/nature10719.

27.

A mechanism for tunable autoinhibition in the structure of a human Ca2+/calmodulin- dependent kinase II holoenzyme.

Chao LH, Stratton MM, Lee IH, Rosenberg OS, Levitz J, Mandell DJ, Kortemme T, Groves JT, Schulman H, Kuriyan J.

Cell. 2011 Sep 2;146(5):732-45. doi: 10.1016/j.cell.2011.07.038. Erratum in: Cell. 2011 Oct 28;147(3):704.

28.

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

Smith CA, Kortemme T.

PLoS One. 2011;6(7):e20451. doi: 10.1371/journal.pone.0020451. Epub 2011 Jul 18.

29.

Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface.

Babor M, Mandell DJ, Kortemme T.

Protein Sci. 2011 Jun;20(6):1082-9. doi: 10.1002/pro.632. Epub 2011 May 3.

30.

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

Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P.

Methods Enzymol. 2011;487:545-74. doi: 10.1016/B978-0-12-381270-4.00019-6.

31.

Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli.

Moon TS, Clarke EJ, Groban ES, Tamsir A, Clark RM, Eames M, Kortemme T, Voigt CA.

J Mol Biol. 2011 Feb 18;406(2):215-27. doi: 10.1016/j.jmb.2010.12.019. Epub 2010 Dec 23.

32.

SNX27 mediates PDZ-directed sorting from endosomes to the plasma membrane.

Lauffer BE, Melero C, Temkin P, Lei C, Hong W, Kortemme T, von Zastrow M.

J Cell Biol. 2010 Aug 23;190(4):565-74. doi: 10.1083/jcb.201004060.

33.

Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains.

Smith CA, Kortemme T.

J Mol Biol. 2010 Sep 17;402(2):460-74. doi: 10.1016/j.jmb.2010.07.032. Epub 2010 Jul 21.

PMID:
20654621
34.

RosettaBackrub--a web server for flexible backbone protein structure modeling and design.

Lauck F, Smith CA, Friedland GF, Humphris EL, Kortemme T.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W569-75. doi: 10.1093/nar/gkq369. Epub 2010 May 12.

35.

Designing ensembles in conformational and sequence space to characterize and engineer proteins.

Friedland GD, Kortemme T.

Curr Opin Struct Biol. 2010 Jun;20(3):377-84. doi: 10.1016/j.sbi.2010.02.004. Epub 2010 Mar 19. Review.

PMID:
20303740
36.

Computer-aided design of functional protein interactions.

Mandell DJ, Kortemme T.

Nat Chem Biol. 2009 Nov;5(11):797-807. doi: 10.1038/nchembio.251. Review.

PMID:
19841629
37.

Backbone flexibility in computational protein design.

Mandell DJ, Kortemme T.

Curr Opin Biotechnol. 2009 Aug;20(4):420-8. doi: 10.1016/j.copbio.2009.07.006. Epub 2009 Aug 24. Review.

PMID:
19709874
38.

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling.

Mandell DJ, Coutsias EA, Kortemme T.

Nat Methods. 2009 Aug;6(8):551-2. doi: 10.1038/nmeth0809-551. No abstract available.

39.

A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T.

PLoS Comput Biol. 2009 May;5(5):e1000393. doi: 10.1371/journal.pcbi.1000393. Epub 2009 May 29.

40.

Complex topology rather than complex membership is a determinant of protein dosage sensitivity.

Oberdorf R, Kortemme T.

Mol Syst Biol. 2009;5:253. doi: 10.1038/msb.2009.9. Epub 2009 Mar 17.

41.

Outcome of a workshop on applications of protein models in biomedical research.

Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA.

Structure. 2009 Feb 13;17(2):151-9. doi: 10.1016/j.str.2008.12.014.

43.

Differences in flexibility underlie functional differences in the Ras activators son of sevenless and Ras guanine nucleotide releasing factor 1.

Freedman TS, Sondermann H, Kuchment O, Friedland GD, Kortemme T, Kuriyan J.

Structure. 2009 Jan 14;17(1):41-53. doi: 10.1016/j.str.2008.11.004.

44.

Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design.

Humphris EL, Kortemme T.

Structure. 2008 Dec 10;16(12):1777-88. doi: 10.1016/j.str.2008.09.012.

45.

Engineered protein connectivity to actin mimics PDZ-dependent recycling of G protein-coupled receptors but not its regulation by Hrs.

Lauffer BE, Chen S, Melero C, Kortemme T, von Zastrow M, Vargas GA.

J Biol Chem. 2009 Jan 23;284(4):2448-58. doi: 10.1074/jbc.M806370200. Epub 2008 Nov 10.

46.

A simple model of backbone flexibility improves modeling of side-chain conformational variability.

Friedland GD, Linares AJ, Smith CA, Kortemme T.

J Mol Biol. 2008 Jul 18;380(4):757-74. doi: 10.1016/j.jmb.2008.05.006. Epub 2008 May 11.

47.

Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction.

Smith CA, Kortemme T.

J Mol Biol. 2008 Jul 18;380(4):742-56. doi: 10.1016/j.jmb.2008.05.023. Epub 2008 May 17.

48.

A new twist in TCR diversity revealed by a forbidden alphabeta TCR.

McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK.

J Mol Biol. 2008 Feb 1;375(5):1306-19. Epub 2007 Nov 17.

50.

Design of multi-specificity in protein interfaces.

Humphris EL, Kortemme T.

PLoS Comput Biol. 2007 Aug;3(8):e164. Epub 2007 Jul 5.

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