Publications

Pre-prints
  1. Akpinaroglu, D., Seki, K., Guo, A., Zhu, E., Kelly M., Kortemme, T. (2024). Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space. bioRxiv 2023.12.15.571823; doi: https://doi.org/10.1101/2023.12.15.571823
  2. Guo, A. B., Akpinaroglu, D., Kelly, M. J. S., Kortemme, T. (2024). Deep learning guided design of dynamic proteins. bioRxiv  2024.07.17.603962; https://doi.org/10.1101/2024.07.17.603962

2024 Publications
  1. Kortemme, T. (2024). De novo protein design—From new structures to programmable functions. Cell, 187 (3), 526–544. https://doi.org/10.1016/j.cell.2023.12.028.
  2. Hong, L., Kortemme, T. (2024). An integrative approach to protein sequence design through multiobjective optimization. PLoS Comput. Biol., 20(7), e1011953. https://doi.org/10.1371/journal.pcbi.1011953.
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2023 Publications
  1. Kretschmer, S., Perry, N., Zhang, Y., and Kortemme, T. Multi-input Drug-Controlled Switches of Mammalian Gene Expression Based on Engineered Nuclear Hormone Receptors. 2023 ACS Synthetic Biology, Article ASAP. https://doi.org/10.1021/acssynbio.3c00080
  2. Mathy CJP, Kortemme T. Emerging maps of allosteric regulation in cellular networks. Curr Opin Struct Biol. 2023 Jun;80:102602. doi: 10.1016/j.sbi.2023.102602. 
  3. Mathy, C. J. P., Mishra, P., Flynn, J. M., Perica, T., Mavor, D., Bolon, D. N. A., & Kortemme, T. (2023). A complete allosteric map of a GTPase switch in its native cellular network. Cell Systems, 14(3), 237-246.e7. https://doi.org/10.1016/j.cels.2023.01.003
  4. Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech TH Jr, Lui I, Laurie MT, Glasgow J, Le CQ, Zhang Y, Diwanji D, Hernandez E, Lopez J, Mehmood H, Pawar KI, Pourmal S, Smith AM, Zhou F; QCRG Structural Biology Consortium; DeRisi J, Kortemme T, Rosenberg OS, Glasgow A, Leung KK, Wells JA, Verba KA. Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. Structure. 2023 Mar 2;31(3):253-264.e6. doi: 10.1016/j.str.2023.01.009. 
  5. Glasgow, A., Hobbs, H.T., Perry, Z.R. et al. Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor. Nat Commun 14, 1179 (2023). https://doi.org/10.1038/s41467-023-36798-1

2022 Publications
  1. Kretschmer S & Kortemme T. Advances in the Computational Design of Small-Molecule-Controlled Protein-Based Circuits for Synthetic Biology. 2022 Proceedings of the IEEE. https://doi.org/10.1109/JPROC.2022.3157898
  2. Krivacic C*, Kundert K*, Pan X*, Pache RA*, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, & Kortemme T.  Accurate positioning of functional residues with robotics-inspired computational protein design. Proc Natl Acad Sci U S A, 2022;119(11), e2115480119. https://doi.org/10.1073/pnas.2115480119 *co-first author
  3. Alberstein RG*, Guo AB*, Kortemme T. Design principles of protein switches. Current Opinion in Structural Biology. 2022 Feb 1;72:71-8. https://doi.org/10.1016/j.sbi.2021.08.004. *co-first author

2021 Publications
  1. Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Conchúir SO, Roy Burman S, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R,  DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature communications, 2021 12(1), 1-15. https://doi.org/10.1038/s41467-021-27222-7
  2. Pan X, Kortemme T. De novo protein fold families expand the designable ligand binding site space. PLoS Comput Biol. 2021 Nov. https://doi.org/10.1371/journal.pcbi.1009620
  3. Perica T*, Mathy CJP*, Xu J, Jang GΜ, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T. Systems-level effects of allosteric perturbations to a model molecular switch. Nature. 2021 Oct 13:1-6. https://doi.org/10.1038/s41586-021-03982-6. *co-first author
  4. Pan X, Kortemme T. Recent advances in de novo protein design: principles, methods, and applications. Journal of Biological Chemistry. 2021 Mar 18:100558. https://doi.org/10.1016/j.jbc.2021.100558

2020 Publications
  1. Gordon DE et al. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). https://doi.org/10.1126/science.abe9403. 
  2. Glasgow A*, Glasgow J*, Limonta D, Solomon P, Lui I, Zhang Y, Nix MA, Rettko NJ., Zha S, Yamin R, Kao K, Rosenberg OS, Ravetch JV, Wiita AP, Leung KK, Lim SA, Zhou XX, Hobman TC, Kortemme T, Wells JA. Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. Proc Natl Acad Sci U S A. 2020;117: 28046–28055. https://doi.org/10.1073/pnas.2016093117. *co-first author
  3. Lucas JE, Kortemme T. New computational protein design methods for de novo small molecule binding sites. PLoS computational biology. 2020 Oct 5;16(10):e1008178. https://doi.org/10.1371/journal.pcbi.1008178
  4. Pan X, Thompson M, Zhang Y, Lin L, Fraser JS, Kelly MJ, Kortemme T. Expanding the space of protein geometries by computational design of de novo fold families. Science. Aug 28;2020 369(6507):1132-1136. doi: 10.1126/science.abc0881.
  5. Bouhaddou M et al. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 Jun 28:S0092-8674(20)30811-4. doi: 10.1016/j.cell.2020.06.034.
  6. Thompson S, Zhang Y, Ingle C, Reynolds KA, Kortemme T. Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme. Elife. 2020 Jul 23;9:e53476. doi:10.7554/eLife.53476.
  7. Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods. 2020 Jul;17(7):665-680. doi: 10.1038/s41592-020-0848-2.
  8. Gordon DE et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Jul;583(7816):459-468. doi: 10.1038/s41586-020-2286-9. *co-first author
  9. Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J; RosettaCommons Consortium, Bystroff C, Schief W, Gront D, Schueler-Furman O, Baker D, Bradley P, Dunbrack R, Kortemme T, Leaver-Fay A, Strauss CEM, Meiler J, Kuhlman B, Gray JJ, Bonneau R. Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput Biol. 2020 May 4;16(5):e1007507. doi: 10.1371/journal.pcbi.1007507. 

2019 Publications
  1. Glasgow AA*, Huang YM*, Mandell DJ*, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. Computational design of a modular protein sense-response system. Science. 2019 Nov 22;366(6468):1024-1028. doi: 10.1126/science.aax8780. *co-first author
  2. Loshbaugh AL, Kortemme T. Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions. Proteins. 2019 Jul 25. doi: 10.1002/prot.25790. 
  3. Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 2019 May 9;10(1):2127. doi: 10.1038/s41467-019-09985-2.
  4. Nguyen HQ, Roy J, Harink B, Damle NP, Latorraca NR, Baxter BC, Brower K, Longwell SA, Kortemme T, Thorn KS, Cyert MS, Fordyce PM. Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads. Elife. 2019 Jul 8;8. pii: e40499. doi: 10.7554/eLife.40499. 
  5. Kundert K, Kortemme T. Computational design of structured loops for new protein functions. Biol Chem. 2019 Feb 25;400(3):275-288. doi: 10.1515/hsz-2018-0348.

2018 Publications
  1. Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open. pii: bio036103. 2018. doi: 10.1242/bio.036103. 
  2. Barlow ,KA, Ó Conchúir, S, Thompson, S, Suresh, P, Lucas, JE, Heinonen, M, Kortemme, T. Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. J Phys Chem B. 2018 doi: 10.1021/acs.jpcb.7b11367. 
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2017 Publications
  1. Smart, AD, Pache ,RA, Thomsen, ND, Kortemme, T, Davis, GW, Wells, JA. Engineering a light-activated caspase-3 for precise ablation of neurons in vivo. Proc Natl Acad Sci. 114(39):E8174-E8183. 2017. doi: 10.1073/pnas.1705064114. 
  2. Bandaru, P, Shah, NH, Bhattacharyya, M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Deconstruction of the Ras switching cycle through saturation mutagenesis. Elife. 6. pii: e27810. 2017.  doi: 10.7554/eLife.27810. 
  3. 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. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. J Chem Theory Comput. 13(6):3031-3048. 2017 doi: 10.1021/acs.jctc.7b00125. 
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2016 Publications
  1. Mavor, D, Barlow, KA, Thompson, S, Barad, BA, Bonny, AR, Cario, CL, Gaskins, G, Liu, Z, Deming, L, Axen, SD, Caceres, E, Chen, W, Cuesta, A, Gate, R, 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, E, See, S, Subramaniam, M, Wong, AW, Li, J, Thorn, KS, Ó Conchúir, S, Roscoe, BP, Chow, ED, DeRisi, JL, Kortemme, T, Bolon, DN, Fraser, JS. Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting. Elife. pii: e15802. 2016. doi: 10.7554/eLife.15802​
  2. Ritterson, RS, Hoersch, D, Barlow, KA, Kortemme, T. Design of Light-Controlled Protein Conformations and Functions. Methods Mol Biol. 1414:197-211, 2016. doi:10.1007/978-1-4939-3569-7_12
  3. Hoersch, D, Kortemme, T. A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine. Structure. 2016 Apr 5;24(4):576-84. Epub 2016 Mar 24. doi:10.1016/j.str.2016.02.015

​2015 Publications
  1. Ollikainen, N, de Jong, RM, Kortemme, T. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. PLoS Comput Biol. 2015 Sep 23;11(9):e1004335. doi: 10.1371/journal.pcbi.1004335
  2. Ó Conchúir*, S, Barlow, KA*, Pache, RA, Ollikainen, N, Kundert, K, O'Meara, MJ, Smith, CA, Kortemme, T. A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PLoS One. 2015 Sep 3;10(9):e0130433. doi: 10.1371/journal.pone.0130433 *co-first author
  3. O'Meara, MJ, Leaver-Fay, A, Tyka, M, Stein, A, Houlihan, K, DiMaio, F, Bradley, P, Kortemme, T, Baker, D, Snoeyink, J, Kuhlman, B. A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta. J Chem Theory Comput. 2015;11(2):609-622. doi: 10.1021/ct500864r

​2014 Publications
  1. Melero, C*, Ollikainen, N*, Harwood, I, Karpiak, J, Kortemme, T. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15426-31. doi: 10.1073/pnas.1410624111. *co-first author
  2. Koide, S, Kortemme, T. Editorial overview: Engineering and design: raising the bar through innovation and integration. Curr Opin Struct Biol. 2014 Aug;27:vi-viii. doi: 10.1016/j.sbi.2014.08.004​ 

​​2013 Publications
  1. Jackson, EL, Ollikainen, N, Covert, AW 3rd, Kortemme, T, Wilke, CO. Amino-acid site variability among natural and designed proteins. PeerJ. 2013 Nov 12;1:e211. doi: 10.7717/peerj.211
  2. Ollikainen, N, Kortemme, T. Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation. PLoS Comput Biol 9(11):e1003313. doi: 10.1371/journal.pcbi.1003313
  3. Hoersch, D, Roh, S, Chiu, W, Kortemme, T. Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nat Nano 8(12):928-32. doi: 10.1038/nnano.2013.242
  4. Ritterson, RS, Kuchenbecker, KM, Michalik, M, Kortemme, T. Design of a Photoswitchable Cadherin. J Am Chem Soc 135(34):12516-9.
  5. Stein, A, Kortemme, T. Improvements to Robotics-Inspired Conformational Sampling in Rosetta. PLoS ONE 8(5):e63090. doi: 10.1371/journal.pone.0063090
  6. Lyskov, S, Chou, F, Ó Conchúir, S, 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. Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE). PLoS ONE 8(5):e63906. doi: 10.1371/journal.pone.0063906
  7. Smith, CA, Shi, CA, Chroust, MK, Bliska, TE, Kelly, MJS, Jacobson, MP, Kortemme, T. Design of a Phosphorylatable PDZ Domain with Peptide-Specific Affinity Changes. Structure 21(1):54-64. doi: 10.1016/j.str.2012.10.007
  8. Ollikainen, N, Smith, CA, Fraser, JS, Kortemme, T. Chapter Four - Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations in Methods in Enzymology Volume 523 (Methods in Protein Design):61-85. doi: 10.1016/B978-0-12-394292-0.00004-7
  9. 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. Chapter Six - Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement in Methods in Enzymology Volume 523 (Methods in Protein Design):109-43. doi: 10.1016/B978-0-12-394292-0.00006-0
 
2012 Publications
  1. Humphris-Narayanan, EL*, Akiva, E*, Varela, R, Ó Conchúir, S, Kortemme, T. Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design. PLoS Comput Biol 8(8):e1002639. doi: 10.1371/journal.pcbi.1002639 *co-first author
  2. Eames, M, Kortemme, T. Cost-Benefit Tradeoffs in Engineered lac Operons. Science 336(6083):911-5. doi: 10.1126/science.1219083 [free download]
  3. Kapp, GT*, Liu, S*, Stein, A, Wong, DT, Reményi, A, Yeh, BJ, Fraser, JS, Taunton, J, Lim, WA, Kortemme, T. Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A :5277-82. doi: 10.1073/pnas.1114487109 *co-first author
 
2011 Publications
  1. Jager, 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, AL, Sali, A, Frankel, AD, Krogan, NJ. Global landscape of HIV-human protein complexes. Nature 481(7381):365-70. doi: 10.1038/nature10719
  2. Chao, LH, Stratton, MM, Lee, I, Rosenberg, OS, Levitz, J, Mandell, DJ, Kortemme, T, Groves, JT, Schulman, H, Kuriyan, J. A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca2+/Calmodulin- Dependent Kinase II Holoenzyme. Cell 146(5):732-45. doi: 10.1016/j.cell.2011.07.038
  3. Smith, CA, Kortemme, T. Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design. PLoS ONE 6(7):e20451. doi: 10.1371/journal.pone.0020451
  4. Babor, M, Mandell, DJ, Kortemme, T. Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin–HER2 interface. Protein Sci 20(6):1082-9. doi:10.1002/pro.632
  5. Leaver-Fay, A, Tyka, M, Lewis, SM, Lange, OF, Thompson, J, Jacak, R, Kaufman, KW, Renfrew, PD, Smith, CA, Sheffler, W, Davis, IW, Cooper, S, Treuille, A, Mandell, DJ, Richter, F, Ban, YA, 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. Chapter nineteen - Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules in Methods in Enzymology Volume 487 (Computer Methods, Part C):545-74. doi: 10.1016/B978-0-12-381270-4.00019-6
  6. Moon, TS, Clarke, EJ, Groban, ES, Tamsir, A, Clark, RM, Eames, M, Kortemme, T, Voigt, CA. Construction of a Genetic Multiplexer to Toggle between Chemosensory Pathways in Escherichia coli. J Mol Biol 406(2):215-27. doi:10.1016/j.jmb.2010.12.019
 
​2010 Publications
  1. Smith, CA, Kortemme, T. Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains. J Mol Biol 402(2):460-74. doi: 10.1016/j.jmb.2010.07.032
  2. Lauffer, BEL, Melero, C, Temkin, P, Lei, C, Hong, W, Kortemme, T, von Zastrow, M. SNX27 mediates PDZ-directed sorting from endosomes to the plasma membrane. J Cell Biol 190(4):565-74. doi: 10.1083/jcb.201004060
  3. Lauck, F, Smith, CA, Friedland, GD, Humphris, EL, Kortemme, T. RosettaBackrub—a web server for flexible backbone protein structure modeling and design. Nucleic Acids Res 38(suppl 2):W569-75. doi: 10.1093/nar/gkq369
  4. Friedland, GD, Kortemme, T. Designing ensembles in conformational and sequence space to characterize and engineer proteins. Curr Opin Struct Biol 20 (Nucleic acids / Sequences and topology)(3):377-84. doi:10.1016/j.sbi.2010.02.004
 
​2009 Publications
  1. Ollikainen, N, Sentovich, E, Coelho, C, Kuehlmann, A, Kortemme, T. SAT-based protein design. Proceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design (ICCAD 2009) (Computer-Aided Design - Digest of Technical Papers, 2009. ICCAD 2009. IEEE/ACM International Conference on):128-35.
  2. Mandell, DJ, Kortemme, T. Computer-aided design of functional protein interactions. Nat Chem Biol 5(11):797-807. doi: 10.1038/nchembio.251
  3. Mandell, DJ, Kortemme, T. Backbone flexibility in computational protein design. Curr Opin Biotechnol 20 (Protein technologies / Systems and synthetic biology)(4):420-8. doi: 10.1016/j.copbio.2009.07.006
  4. Mandell, DJ, Coutsias, EA, Kortemme, T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 6(8):551-2. doi: 10.1038/nmeth0809-551
  5. Friedland, GD, Lakomek, N, Griesinger, C, Meiler, J, Kortemme, T. A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family. PLoS Comput Biol 5(5):e1000393. doi: 10.1371/journal.pcbi.1000393
  6. Oberdorf, R, Kortemme, T. Complex topology rather than complex membership is a determinant of protein dosage sensitivity. Mol Syst Biol 5(253). doi: 10.1038/msb.2009.9
  7. Schwede, T, Sali, A, Honig, B, Levitt, M, Berman, HM, Jones, D, Brenner, SE, Burley, SK, Das, R, Dokholyan, NV, Dunbrack Jr., RL, Fidelis, K, Fiser, A, Godzik, A, Huang, YJ, Humblet, C, Jacobson, MP, Joachimiak, A, Krystek Jr., SR, 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. Outcome of a Workshop on Applications of Protein Models in Biomedical Research. Structure 17(2):151-9. doi: 10.1016/j.str.2008.12.014
  8. Babor, M, Kortemme, T. Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. Proteins 75(4):846-58. doi: 10.1002/prot.22293
  9. Freedman, TS, Sondermann, H, Kuchment, O, Friedland, GD, Kortemme, T, Kuriyan, J. Differences in Flexibility Underlie Functional Differences in the Ras Activators Son of Sevenless and Ras Guanine Nucleotide Releasing Factor 1. Structure 17(1):41-53. doi: 10.1016/j.str.2008.11.004
 
​2008 Publications
  1. Humphris, EL, Kortemme, T. Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design. Structure 16(12):1777-88. doi: 10.1016/j.str.2008.09.012
  2. Lauffer, BEL, Chen, S, Melero, C, Kortemme, T, von Zastrow, M, Vargas, GA. Engineered Protein Connectivity to Actin Mimics PDZ-dependent Recycling of G Protein-coupled Receptors but Not Its Regulation by Hrs. J Biol Chem 284(4):2448-58. doi: 10.1074/jbc.M806370200
  3. Friedland, GD, Linares, AJ, Smith, CA, Kortemme, T. A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability. J Mol Biol 380(4):757-74. doi: 10.1016/j.jmb.2008.05.006
  4. Smith, CA, Kortemme, T. Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction. J Mol Biol 380(4):742-56. doi: 10.1016/j.jmb.2008.05.023
  5. McBeth, C, Seamons, A, Pizarro, JC, Fleishman, SJ, Baker, D, Kortemme, T, Goverman, JM, Strong, RK. A New Twist in TCR Diversity Revealed by a Forbidden αβ TCR. J Mol Biol 375(5):1306-19. doi: 10.1016/j.jmb.2007.11.020
 
​2007 Publications
  1. Humphris, EL, Kortemme, T. Design of Multi-Specificity in Protein Interfaces. PLoS Comput Biol 3(8):1591-604. doi: 10.1371/journal.pcbi.0030164
  2. Lengyel, CSE, Willis, LJ, Mann, P, Baker, D, Kortemme, T, Strong, RK, McFarland, BJ. Mutations Designed to Destabilize the Receptor-Bound Conformation Increase MICA-NKG2D Association Rate and Affinity. J Biol Chem 282(42):30658-66. doi: 10.1074/jbc.M704513200
  3. Eames, M, Kortemme, T. Structural Mapping of Protein Interactions Reveals Differences in Evolutionary Pressures Correlated to mRNA Level and Protein Abundance. Structure 15(11):1442-51. doi: 10.1016/j.str.2007.09.010
 
​2006 Publications
  1. Joachimiak, LA, Kortemme, T, Stoddard, BL, Baker, D. Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein−Protein Interface. J Mol Biol 361(1):195-208. doi:10.1016/j.jmb.2006.05.022
  2. Palmer, AE, Giacomello, M, Kortemme, T, Hires, SA, Lev-Ram, V, Baker, D, Tsien, RY. Ca2+ Indicators Based on Computationally Redesigned Calmodulin-Peptide Pairs. Chem Biol 13(5):521-30. doi:10.1016/j.chembiol.2006.03.007
  3. Song, G, Lazar, GA, Kortemme, T, Shimaoka, M, Desjarlais, JR, Baker, D, Springer, TA. Rational Design of Intercellular Adhesion Molecule-1 (ICAM-1) Variants for Antagonizing Integrin Lymphocyte Function-associated Antigen-1-dependent Adhesion. J Biol Chem 281(8):5042-9. doi: 10.1074/jbc.M510454200
  4. Freedman, TS, Sondermann, H, Friedland, GD, Kortemme, T, Bar-Sagi, D, Marqusee, S, Kuriyan, J. A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc Natl Acad Sci U S A 103(45):16692-7. doi:10.1073/pnas.0608127103
  5. Wang, SX, Pandey, KC, Somoza, JR, Sijwali, PS, Kortemme, T, Brinen, LS, Fletterick, RJ, Rosenthal, PJ, McKerrow, JH. Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease. Proc Natl Acad Sci U S A 103(31):11503-8. doi: 10.1073/pnas.0600489103
 
​2005 Publications
  1. Morozov, AV, Kortemme, T. Potential Functions for Hydrogen Bonds in Protein Structure Prediction and Design in Advances in Protein Chemistry Volume 72 (Peptide Solvation and H‐Bonds):1-38. doi: 10.1016/S0065-3233(05)72001-5
 
​Prediction and Design of Protein-Protein Interactions
  1. Kortemme, T, Baker, D. A simple physical model for binding energy hot spots in protein–protein complexes. Proc Natl Acad Sci U S A 99(22):14116-21, 2002. doi: 10.1073/pnas.202485799
  2. Chevalier, BS, Kortemme, T, Chadsey, MS, Baker, D, Monnat Jr., RJ, Stoddard, BL. Design, Activity, and Structure of a Highly Specific Artificial Endonuclease. Mol Cell 10(4):895-905, 2002. doi: 10.1016/S1097-2765(02)00690-1
  3. Gray, JJ, Moughon, SE, Kortemme, T, Schueler-Furman, O, Misura, KMS, Morozov, AV, Baker, D. Protein–protein docking predictions for the CAPRI experiment. Proteins 52(1):118-22, 2003. doi: 10.1002/prot.10384
  4. Kortemme, T*, Joachimiak, LA*, Bullock, AN*, Schuler, AD, Stoddard, BL, Baker, D. Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol 11(4):371-9, 2004. doi: 10.1038/nsmb749 *co-first author
  5. Kortemme, T, Baker, D. Computational design of protein–protein interactions. Curr Opin Chem Biol 8(1):91-7, 2004. doi: 10.1016/j.cbpa.2003.12.008
 
​Computational Models & Energy Functions
  1. Kortemme, T, Morozov, AV, Baker, D. An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes. J Mol Biol 326(4):1239-59, 2003. doi:10.1016/S0022-2836(03)00021-4
  2. Morozov, AV, Kortemme, T, Baker, D. Evaluation of Models of Electrostatic Interactions in Proteins. J Phys Chem B 107 (The Journal of Physical Chemistry B)(9):2075-90, 2003. doi: 10.1021/jp0267555
  3. Kortemme, T, Kim, DE, Baker, D. Computational Alanine Scanning of Protein-Protein Interfaces. Sci STKE 2004(219):pl2, 2004. doi: 10.1126/stke.2192004pl2
  4. Morozov, AV, Kortemme, T, Tsemekhman, K, Baker, D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci U S A 101(18):6946-51, 2004. doi: 10.1073/pnas.0307578101
  5. Chen, Y, Kortemme, T, Robertson, T, Baker, D, Varani, G. A new hydrogen-bonding potential for the design of protein–RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res 32(17):5147-62, 2004. doi: 10.1093/nar/gkh785
  6. Jiang, L, Kuhlman, B, Kortemme, T, Baker, D. A “solvated rotamer” approach to modeling water-mediated hydrogen bonds at protein–protein interfaces. Proteins 58(4):893-904, 2005. doi: 10.1002/prot.20347

Predictions on Specific Systems
  1. McFarland, BJ, Kortemme, T, Yu, SF, Baker, D, Strong, RK. Symmetry Recognizing Asymmetry: Analysis of the Interactions between the C-Type Lectin-like Immunoreceptor NKG2D and MHC Class I-like Ligands. Structure 11(4):411-22, 2003. doi: 10.1016/S0969-2126(03)00047-9
  2. Boulanger, MJ, Bankovich, AJ, Kortemme, T, Baker, D, Garcia, KC. Convergent Mechanisms for Recognition of Divergent Cytokines by the Shared Signaling Receptor gp130. Mol Cell 12(3):577-89, 2003. doi: 10.1016/S1097-2765(03)00365-4
  3. Svensson, HG, Wedemeyer, WJ, Ekstrom, JL, Callender, DR, Kortemme, T, Kim, DE, Sjöbring, U, Baker, D. Contributions of Amino Acid Side Chains to the Kinetics and Thermodynamics of the Bivalent Binding of Protein L to Ig κ Light Chain. Biochemistry 43 (Biochemistry)(9):2445-57, 2004. doi: 10.1021/bi034873s
 
Peptide Model Systems: Alpha-helices and Beta-sheets
  1. Chakrabartty, A, Kortemme, T, Padmanabhan, S, Baldwin, RL. Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities. Biochemistry 32 (Biochemistry)(21):5560-5, 1993. doi: 10.1021/bi00072a010
  2. Chakrabartty, A, Kortemme, T, Baldwin, RL. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 3(5):843-52, 1994. doi: 10.1002/pro.5560030514
  3. Kortemme, T*, Ramı́rez-Alvarado, M*, Serrano, L. Design of a 20-Amino Acid, Three-Stranded β-Sheet Protein. Science 281(5374):253-6, 1998. doi: 10.1126/science.281.5374.253 *co-first author
  4. Ramı́rez-Alvarado, M, Kortemme, T, Blanco, FJ, Serrano, L. β-Hairpin and β-sheet formation in designed linear peptides. Bioorg Med Chem 7(1):93-103, 1999. doi: 10.1016/S0968-0896(98)00215-6
  5. Lacroix, E, Kortemme, T, de la Paz, ML, Serrano, L. The design of linear peptides that fold as monomeric β-sheet structures. Curr Opin Struct Biol 9(4):487-93, 1999. doi: 10.1016/S0959-440X(99)80069-4
 
Protein Folding
  1. Kortemme, T, Hollecker, M, Kemmink, J, Creighton, TE. Comparison of the (30-51, 14-38) Two-disulphide Folding Intermediates of the Homologous Proteins Dendrotoxin K and Bovine Pancreatic Trypsin Inhibitor by Two-dimensional1H Nuclear Magnetic Resonance. J Mol Biol 257(1):188-98, 1996. doi: 10.1006/jmbi.1996.0155
  2. Kortemme, T, Kelly, MJS, Kay, LE, Forman-Kay, J, Serrano, L. Similarities between the spectrin SH3 domain denatured state and its folding transition state. J Mol Biol 297(5):1217-29, 2000. doi: 10.1006/jmbi.2000.3618
  3. Alm, E, Morozov, AV, Kortemme, T, Baker, D. Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics. J Mol Biol 322(2):463-76, 2002. doi: 10.1016/S0022-2836(02)00706-4

Electrostatic interactions in Thioredoxin-like Proteins
  1. Kortemme, T, Creighton, TE. Ionisation of Cysteine Residues at the Termini of Model α-Helical Peptides. Relevance to Unusual Thiol pKa Values in Proteins of the Thioredoxin Family. J Mol Biol 253(5):799-812, 1995. doi:10.1006/jmbi.1995.0592
  2. Kortemme, T, Darby, NJ, Creighton, TE. Electrostatic Interactions in the Active Site of the N-Terminal Thioredoxin-like Domain of Protein Disulfide Isomerase. Biochemistry 35 (Biochemistry)(46):14503-11, 1996. doi:10.1021/bi9617724
  3. Bulaj, G, Kortemme, T, Goldenberg, DP. Ionization−Reactivity Relationships for Cysteine Thiols in Polypeptides. Biochemistry 37 (Biochemistry)(25):8965-72, 1998. doi: 10.1021/bi973101r