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Tanja Kortemme, PhD

Title(s)Professor, Bioengineering
SchoolSchool of Pharmacy
Address1700 4th Street
San Francisco CA 94158
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    Collapse Biography 
    Collapse Awards and Honors
    Chan Zuckerberg Biohub2017Investigator
    W.M. Keck Foundation2013Medical Research Award
    Gen920121st Place, G-Prize
    National Science Foundation (NSF)2008CAREER Award
    Alfred P. Sloan Foundation2005Junior Faculty Award
    Human Frontiers Science Program (HFSP)2000Postdoctoral Fellow
    European Molecular Biology Organization (EMBO)1999Postdoctoral Fellow
    European Molecular Biology Laboratory (EMBL)1993Graduate Fellow
    German National Academic Foundation ("Studienstiftung des Deutschen Volkes")1989Scholar

    Collapse Overview 
    Collapse Overview
    Engineered biological systems, ranging from molecules with new functions to entire organisms, have tremendous practical importance; they can also fundamentally change how we ask questions about the biological principles of function and fitness. Our research aims to invent approaches to engineer new molecules that operate as predicted in biological contexts, and to utilize prediction and engineering to address fundamental questions on the relationship of molecular characteristics, cellular function and organismal fitness. To address the many current challenges in the field – from developing more predictive computational design methods to determining the requirements for function in cells – we combine concepts from computer science, physics, chemistry, mathematics, engineering and biology.

    Our work spans three interrelated themes:

    I. Develop computational methods for modeling & design of proteins, in the program Rosetta (www.rosettacommons.org).

    Predicting and designing the structures of proteins with biologically useful accuracy has been a key challenge in computational structural biology and molecular engineering. We have made methodological advances that address one of the main bottlenecks: sampling the vast number of conformations accessible to proteins. We have utilized a method for moving through conformational space inspired by principles from robotics – a field with a rich history in efficient calculation of mechanically accessible states subject to constraints. We applied the same mathematics that can be used to direct the motions of a robot arm to compute the degrees of freedom of a polypeptide chain (Mandell et al., Nature Methods 2009). Our predictions generate hypotheses on protein conformations controlling biological processes – such as protein recognition, signal transduction, and enzyme active site gating – and are laying the foundation for our work reengineering and “reshaping” protein interfaces and active sites for new functions.

    II. Create new proteins and devices with more advanced functions by experimental engineering.

    Designer molecules with new biological functions could have many exciting uses: protein therapeutics with minimal side effects; new enzymes and biological synthesis pathways for fuel molecules or compounds that are otherwise too expensive to produce; sensor/actuator devices that can report on cell biological processes in real time; robust signaling systems that can detect specific inputs and generate a precise response; protein machines that can be controlled by specific external inputs such as light. Over the past several years, we have engineered a range of proteins with new functions, including protein-protein interactions that are specific enough to control complex biological processes in mammalian cells (Kapp et al., PNAS, 2012). We have also engineered proteins whose functions can be switched by phosphorylation or light. A recent highlight is a study describing the control of precise shape transitions of a large protein assembly with optical inputs, where we successfully exchanged the ‘engine’ of a protein-based ATP-driven molecular machine to be powered by light (Hoersch et al., Nature Nanotechnology 2013). A current focus is to apply computational protein design to create new proteins that can sense molecular signals in living cells and orchestrate desired biological responses.

    III. Dissect design principles of function in cells by combining prediction and engineering approaches.

    Cells must balance the cost and benefit to optimize organismal fitness. In a recent study, we used the lac operon of Escherichia coli – a classic system for regulatory mechanisms that balance cost and benefit of protein expression – to quantify the economics of protein production (Eames & Kortemme, Science 2012). A current experimental effort is directed towards determining the system-level functions of specific interactions in cells and organisms by systematically modulating protein interactions and protein abundance. In a new project, we have begun to characterize large-scale genetic interactions of engineered proteins with altered interaction patterns, using the E-MAP (epistatic mini array profile) technology, in collaboration with Nevan Krogan’s laboratory at UCSF. With Mark von Zastrow's group at UCSF, we have reengineered and characterized PDZ-domain mediated interactions in the recycling of G-protein coupled receptors to quantify the interaction specificities of protein-peptide interactions in the context of cellular processes. These investigations reveal an unexpected functional promiscuity in cellular networks, and suggest that there are biologically important differences between biochemically possible and functionally utilized interactions.

    Collapse Research 
    Collapse Research Activities and Funding
    Computational design of Cas9-based molecular imaging reagents
    NIH/NIBIB R21EB021453May 10, 2016 - Feb 28, 2018
    Role: Principal Investigator
    Discovery of Protein Network Function
    NIH/NIGMS R01GM117189Jan 1, 2016 - Dec 31, 2019
    Role: Principal Investigator
    Computational design of new protein structures and interactions
    NIH/NIGMS R01GM110089May 1, 2015 - Apr 30, 2019
    Role: Principal Investigator
    Integrating computation and genetics to quantify specificity in protein networks
    NIH/NIGMS R01GM098101Aug 1, 2011 - May 31, 2015
    Role: Co-Principal Investigator
    Computational design of protein-based modular small-molecule biosensors
    NIH/NIBIB R21EB013389Apr 1, 2011 - Mar 31, 2014
    Role: Principal Investigator
    Molecular Biophysics Training Grant
    NIH/NIGMS T32GM008284Sep 30, 1988 - Jun 30, 2023
    Role: Co-Principal Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
    Collapse Websites
    Collapse Academic Senate

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Expanding the space of protein geometries by computational design of de novo fold families. Science. 2020 08 28; 369(6507):1132-1136. Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. PMID: 32855341.
      View in: PubMed   Mentions:    Fields:    
    2. Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. bioRxiv. 2020 Aug 01. Glasgow A, Glasgow J, Limonta D, Solomon P, Lui I, Zhang Y, Nix MA, Rettko NJ, Lim SA, Zha S, Yamin R, Kao K, Rosenberg OS, Ravetch JV, Wiita AP, Leung KK, Zhou XX, Hobman TC, Kortemme T, Wells JA. PMID: 32766586.
      View in: PubMed   Mentions:
    3. 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. Thompson S, Zhang Y, Ingle C, Reynolds KA, Kortemme T. PMID: 32701056.
      View in: PubMed   Mentions:    Fields:    
    4. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 08 06; 182(3):685-712.e19. Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. PMID: 32645325.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    5. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods. 2020 Jul; 17(7):665-680. 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. PMID: 32483333.
      View in: PubMed   Mentions: 2     Fields:    
    6. Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput Biol. 2020 05; 16(5):e1007507. Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, 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. PMID: 32365137.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    7. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. PMID: 32353859.
      View in: PubMed   Mentions: 148     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    8. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. PMID: 32511329.
      View in: PubMed   Mentions:
    9. Computational design of a modular protein sense-response system. Science. 2019 11 22; 366(6468):1024-1028. 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. PMID: 31754004.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    10. Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions. Proteins. 2020 01; 88(1):206-226. Loshbaugh AL, Kortemme T. PMID: 31344278.
      View in: PubMed   Mentions: 1     Fields:    
    11. Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads. Elife. 2019 07 08; 8. Nguyen HQ, Roy J, Harink B, Damle NP, Latorraca NR, Baxter BC, Brower K, Longwell SA, Kortemme T, Thorn KS, Cyert MS, Fordyce PM. PMID: 31282865.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    12. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 2019 05 09; 10(1):2127. 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. PMID: 31073154.
      View in: PubMed   Mentions: 6     Fields:    
    13. Computational design of structured loops for new protein functions. Biol Chem. 2019 02 25; 400(3):275-288. Kundert K, Kortemme T. PMID: 30676995.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    14. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open. 2018 Jul 23; 7(7). 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. PMID: 30037883.
      View in: PubMed   Mentions:
    15. Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. J Phys Chem B. 2018 05 31; 122(21):5389-5399. Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas JE, Heinonen M, Kortemme T. PMID: 29401388.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    16. Engineering a light-activated caspase-3 for precise ablation of neurons in vivo. Proc Natl Acad Sci U S A. 2017 09 26; 114(39):E8174-E8183. Smart AD, Pache RA, Thomsen ND, Kortemme T, Davis GW, Wells JA. PMID: 28893998.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    17. Deconstruction of the Ras switching cycle through saturation mutagenesis. Elife. 2017 07 07; 6. Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. PMID: 28686159.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    18. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. J Chem Theory Comput. 2017 Jun 13; 13(6):3031-3048. 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, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ. PMID: 28430426.
      View in: PubMed   Mentions: 65     Fields:    Translation:Cells
    19. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. Elife. 2016 04 25; 5. 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. PMID: 27111525.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimals
    20. A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine. Structure. 2016 Apr 05; 24(4):576-584. Hoersch D, Kortemme T. PMID: 27021162.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    21. Design of Light-Controlled Protein Conformations and Functions. Methods Mol Biol. 2016; 1414:197-211. Ritterson RS, Hoersch D, Barlow KA, Kortemme T. PMID: 27094293.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    22. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. PLoS Comput Biol. 2015; 11(9):e1004335. Ollikainen N, de Jong RM, Kortemme T. PMID: 26397464.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    23. A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PLoS One. 2015; 10(9):e0130433. Ó Conchúir S, Barlow KA, Pache RA, Ollikainen N, Kundert K, O'Meara MJ, Smith CA, Kortemme T. PMID: 26335248.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    24. Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. J Chem Theory Comput. 2015 Feb 10; 11(2):609-22. O'Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. PMID: 25866491.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    25. 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. Melero C, Ollikainen N, Harwood I, Karpiak J, Kortemme T. PMID: 25313039.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    26. Editorial overview: Engineering and design: raising the bar through innovation and integration. Curr Opin Struct Biol. 2014 Aug; 27:vi-viii. Koide S, Kortemme T. PMID: 25175941.
      View in: PubMed   Mentions:    Fields:    
    27. Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nat Nanotechnol. 2013 Dec; 8(12):928-32. Hoersch D, Roh SH, Chiu W, Kortemme T. PMID: 24270642.
      View in: PubMed   Mentions: 12     Fields:    
    28. Computational protein design quantifies structural constraints on amino acid covariation. PLoS Comput Biol. 2013; 9(11):e1003313. Ollikainen N, Kortemme T. PMID: 24244128.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    29. Amino-acid site variability among natural and designed proteins. PeerJ. 2013; 1:e211. Jackson EL, Ollikainen N, Covert AW, Kortemme T, Wilke CO. PMID: 24255821.
      View in: PubMed   Mentions:
    30. Design of a photoswitchable cadherin. J Am Chem Soc. 2013 Aug 28; 135(34):12516-9. Ritterson RS, Kuchenbecker KM, Michalik M, Kortemme T. PMID: 23923816.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    31. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS One. 2013; 8(5):e63906. 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. PMID: 23717507.
      View in: PubMed   Mentions: 85     Fields:    Translation:Cells
    32. Improvements to robotics-inspired conformational sampling in rosetta. PLoS One. 2013; 8(5):e63090. Stein A, Kortemme T. PMID: 23704889.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    33. Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol. 2013; 523:61-85. Ollikainen N, Smith CA, Fraser JS, Kortemme T. PMID: 23422426.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    34. Scientific benchmarks for guiding macromolecular energy function improvement. Methods Enzymol. 2013; 523:109-43. 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. PMID: 23422428.
      View in: PubMed   Mentions: 75     Fields:    Translation:Cells
    35. Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure. 2013 Jan 08; 21(1):54-64. Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJS, Jacobson MP, Kortemme T. PMID: 23159126.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    36. Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design. PLoS Comput Biol. 2012; 8(8):e1002639. Humphris-Narayanan E, Akiva E, Varela R, Ó Conchúir S, Kortemme T. PMID: 22927804.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    37. Cost-benefit tradeoffs in engineered lac operons. Science. 2012 May 18; 336(6083):911-5. Eames M, Kortemme T. PMID: 22605776.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    38. Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A. 2012 Apr 03; 109(14):5277-82. Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T. PMID: 22403064.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    39. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. 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. PMID: 22190034.
      View in: PubMed   Mentions: 256     Fields:    Translation:HumansCells
    40. A mechanism for tunable autoinhibition in the structure of a human Ca2+/calmodulin- dependent kinase II holoenzyme. Cell. 2011 Sep 02; 146(5):732-45. Chao LH, Stratton MM, Lee IH, Rosenberg OS, Levitz J, Mandell DJ, Kortemme T, Groves JT, Schulman H, Kuriyan J. PMID: 21884935.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansAnimalsCells
    41. Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design. PLoS One. 2011; 6(7):e20451. Smith CA, Kortemme T. PMID: 21789164.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    42. Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface. Protein Sci. 2011 Jun; 20(6):1082-9. Babor M, Mandell DJ, Kortemme T. PMID: 21465611.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    43. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 2011; 487:545-74. 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, Popovic Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P. PMID: 21187238.
      View in: PubMed   Mentions: 522     Fields:    
    44. Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. J Mol Biol. 2011 Feb 18; 406(2):215-27. Moon TS, Clarke EJ, Groban ES, Tamsir A, Clark RM, Eames M, Kortemme T, Voigt CA. PMID: 21185306.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    45. SNX27 mediates PDZ-directed sorting from endosomes to the plasma membrane. J Cell Biol. 2010 Aug 23; 190(4):565-74. Lauffer BE, Melero C, Temkin P, Lei C, Hong W, Kortemme T, von Zastrow M. PMID: 20733053.
      View in: PubMed   Mentions: 107     Fields:    Translation:HumansAnimalsCells
    46. Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. J Mol Biol. 2010 Sep 17; 402(2):460-74. Smith CA, Kortemme T. PMID: 20654621.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    47. RosettaBackrub--a web server for flexible backbone protein structure modeling and design. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W569-75. Lauck F, Smith CA, Friedland GF, Humphris EL, Kortemme T. PMID: 20462859.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    48. Designing ensembles in conformational and sequence space to characterize and engineer proteins. Curr Opin Struct Biol. 2010 Jun; 20(3):377-84. Friedland GD, Kortemme T. PMID: 20303740.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    49. Computer-aided design of functional protein interactions. Nat Chem Biol. 2009 Nov; 5(11):797-807. Mandell DJ, Kortemme T. PMID: 19841629.
      View in: PubMed   Mentions: 68     Fields:    Translation:Cells
    50. Backbone flexibility in computational protein design. Curr Opin Biotechnol. 2009 Aug; 20(4):420-8. Mandell DJ, Kortemme T. PMID: 19709874.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    51. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 2009 Aug; 6(8):551-2. Mandell DJ, Coutsias EA, Kortemme T. PMID: 19644455.
      View in: PubMed   Mentions: 164     Fields:    Translation:Cells
    52. Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. Proteins. 2009 Jun; 75(4):846-58. Babor M, Kortemme T. PMID: 19194863.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    53. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol. 2009 May; 5(5):e1000393. Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T. PMID: 19478996.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    54. Complex topology rather than complex membership is a determinant of protein dosage sensitivity. Mol Syst Biol. 2009; 5:253. Oberdorf R, Kortemme T. PMID: 19293832.
      View in: PubMed   Mentions: 11     Fields:    Translation:Animals
    55. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek 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. PMID: 19217386.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimalsCells
    56. Differences in flexibility underlie functional differences in the Ras activators son of sevenless and Ras guanine nucleotide releasing factor 1. Structure. 2009 Jan 14; 17(1):41-53. Freedman TS, Sondermann H, Kuchment O, Friedland GD, Kortemme T, Kuriyan J. PMID: 19141281.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    57. SAT-based Protein Design. 2009 IEEE/ACM International Conference on Computer-Aided Design Digest of Technical Papers (ICCAD 2009). 2009; 128-35. Ollikainen N, Sentovich E, Coelho C, Kuehlmann A, Kortemme T..
    58. Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure. 2008 Dec 10; 16(12):1777-88. Humphris EL, Kortemme T. PMID: 19081054.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    59. Engineered protein connectivity to actin mimics PDZ-dependent recycling of G protein-coupled receptors but not its regulation by Hrs. J Biol Chem. 2009 Jan 23; 284(4):2448-58. Lauffer BE, Chen S, Melero C, Kortemme T, von Zastrow M, Vargas GA. PMID: 19001361.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    60. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol. 2008 Jul 18; 380(4):742-56. Smith CA, Kortemme T. PMID: 18547585.
      View in: PubMed   Mentions: 110     Fields:    Translation:Cells
    61. A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol. 2008 Jul 18; 380(4):757-74. Friedland GD, Linares AJ, Smith CA, Kortemme T. PMID: 18547586.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    62. A new twist in TCR diversity revealed by a forbidden alphabeta TCR. J Mol Biol. 2008 Feb 01; 375(5):1306-19. McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK. PMID: 18155234.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCellsPHPublic Health
    63. Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. Structure. 2007 Nov; 15(11):1442-51. Eames M, Kortemme T. PMID: 17997970.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    64. Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. J Biol Chem. 2007 Oct 19; 282(42):30658-66. Lengyel CS, Willis LJ, Mann P, Baker D, Kortemme T, Strong RK, McFarland BJ. PMID: 17690100.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    65. Design of multi-specificity in protein interfaces. PLoS Comput Biol. 2007 Aug; 3(8):e164. Humphris EL, Kortemme T. PMID: 17722975.
      View in: PubMed   Mentions: 53     Fields:    Translation:Cells
    66. A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc Natl Acad Sci U S A. 2006 Nov 07; 103(45):16692-7. Freedman TS, Sondermann H, Friedland GD, Kortemme T, Bar-Sagi D, Marqusee S, Kuriyan J. PMID: 17075039.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansAnimalsCells
    67. Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease. Proc Natl Acad Sci U S A. 2006 Aug 01; 103(31):11503-8. Wang SX, Pandey KC, Somoza JR, Sijwali PS, Kortemme T, Brinen LS, Fletterick RJ, Rosenthal PJ, McKerrow JH. PMID: 16864794.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    68. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol. 2006 Aug 04; 361(1):195-208. Joachimiak LA, Kortemme T, Stoddard BL, Baker D. PMID: 16831445.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    69. Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chem Biol. 2006 May; 13(5):521-30. Palmer AE, Giacomello M, Kortemme T, Hires SA, Lev-Ram V, Baker D, Tsien RY. PMID: 16720273.
      View in: PubMed   Mentions: 182     Fields:    Translation:HumansCells
    70. Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. J Biol Chem. 2006 Feb 24; 281(8):5042-9. Song G, Lazar GA, Kortemme T, Shimaoka M, Desjarlais JR, Baker D, Springer TA. PMID: 16354667.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    71. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 2005 Mar 01; 58(4):893-904. Jiang L, Kuhlman B, Kortemme T, Baker D. PMID: 15651050.
      View in: PubMed   Mentions: 50     Fields:    Translation:Cells
    72. Potential functions for hydrogen bonds in protein structure prediction and design. Adv Protein Chem. 2005; 72:1-38. Morozov AV, Kortemme T. PMID: 16581371.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    73. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res. 2004; 32(17):5147-62. Chen Y, Kortemme T, Robertson T, Baker D, Varani G. PMID: 15459285.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    74. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci U S A. 2004 May 04; 101(18):6946-51. Morozov AV, Kortemme T, Tsemekhman K, Baker D. PMID: 15118103.
      View in: PubMed   Mentions: 67     Fields:    Translation:Cells
    75. Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol. 2004 Apr; 11(4):371-9. Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D. PMID: 15034550.
      View in: PubMed   Mentions: 111     Fields:    Translation:Cells
    76. Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. Biochemistry. 2004 Mar 09; 43(9):2445-57. Svensson HG, Wedemeyer WJ, Ekstrom JL, Callender DR, Kortemme T, Kim DE, Sjöbring U, Baker D. PMID: 14992582.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    77. Computational alanine scanning of protein-protein interfaces. Sci STKE. 2004 Feb 03; 2004(219):pl2. Kortemme T, Kim DE, Baker D. PMID: 14872095.
      View in: PubMed   Mentions: 165     Fields:    Translation:Cells
    78. Computational design of protein-protein interactions. Curr Opin Chem Biol. 2004 Feb; 8(1):91-7. Kortemme T, Baker D. PMID: 15036162.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    79. Evaluation of Models of Electrostatic Interactions in Proteins. J. Phys. Chem. B. 2003; 107:2075-90. Morozov AV, Kortemme T, Baker D.
    80. Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130. Mol Cell. 2003 Sep; 12(3):577-89. Boulanger MJ, Bankovich AJ, Kortemme T, Baker D, Garcia KC. PMID: 14527405.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    81. Protein-protein docking predictions for the CAPRI experiment. Proteins. 2003 Jul 01; 52(1):118-22. Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D. PMID: 12784377.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    82. Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands. Structure. 2003 Apr; 11(4):411-22. McFarland BJ, Kortemme T, Yu SF, Baker D, Strong RK. PMID: 12679019.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    83. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol. 2003 Feb 28; 326(4):1239-59. Kortemme T, Morozov AV, Baker D. PMID: 12589766.
      View in: PubMed   Mentions: 172     Fields:    Translation:Cells
    84. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A. 2002 Oct 29; 99(22):14116-21. Kortemme T, Baker D. PMID: 12381794.
      View in: PubMed   Mentions: 273     Fields:    Translation:Cells
    85. Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell. 2002 Oct; 10(4):895-905. Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. PMID: 12419232.
      View in: PubMed   Mentions: 76     Fields:    Translation:Cells
    86. Simple physical models connect theory and experiment in protein folding kinetics. J Mol Biol. 2002 Sep 13; 322(2):463-76. Alm E, Morozov AV, Kortemme T, Baker D. PMID: 12217703.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    87. Similarities between the spectrin SH3 domain denatured state and its folding transition state. J Mol Biol. 2000 Apr 14; 297(5):1217-29. Kortemme T, Kelly MJ, Kay LE, Forman-Kay J, Serrano L. PMID: 10764585.
      View in: PubMed   Mentions: 25     Fields:    Translation:AnimalsCells
    88. The design of linear peptides that fold as monomeric beta-sheet structures. Curr Opin Struct Biol. 1999 Aug; 9(4):487-93. Lacroix E, Kortemme T, Lopez de la Paz M, Serrano L. PMID: 10449370.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    89. Beta-hairpin and beta-sheet formation in designed linear peptides. Bioorg Med Chem. 1999 Jan; 7(1):93-103. Ramírez-Alvarado M, Kortemme T, Blanco FJ, Serrano L. PMID: 10199660.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    90. Design of a 20-amino acid, three-stranded beta-sheet protein. Science. 1998 Jul 10; 281(5374):253-6. Kortemme T, Ramírez-Alvarado M, Serrano L. PMID: 9657719.
      View in: PubMed   Mentions: 63     Fields:    Translation:Cells
    91. Ionization-reactivity relationships for cysteine thiols in polypeptides. Biochemistry. 1998 Jun 23; 37(25):8965-72. Bulaj G, Kortemme T, Goldenberg DP. PMID: 9636038.
      View in: PubMed   Mentions: 55     Fields:    Translation:Cells
    92. Electrostatic interactions in the active site of the N-terminal thioredoxin-like domain of protein disulfide isomerase. Biochemistry. 1996 Nov 19; 35(46):14503-11. Kortemme T, Darby NJ, Creighton TE. PMID: 8931546.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    93. Comparison of the (30-51, 14-38) two-disulphide folding intermediates of the homologous proteins dendrotoxin K and bovine pancreatic trypsin inhibitor by two-dimensional 1H nuclear magnetic resonance. J Mol Biol. 1996 Mar 22; 257(1):188-98. Kortemme T, Hollecker M, Kemmink J, Creighton TE. PMID: 8632454.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    94. Ionisation of cysteine residues at the termini of model alpha-helical peptides. Relevance to unusual thiol pKa values in proteins of the thioredoxin family. J Mol Biol. 1995 Nov 10; 253(5):799-812. Kortemme T, Creighton TE. PMID: 7473753.
      View in: PubMed   Mentions: 76     Fields:    Translation:Cells
    95. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 1994 May; 3(5):843-52. Chakrabartty A, Kortemme T, Baldwin RL. PMID: 8061613.
      View in: PubMed   Mentions: 132     Fields:    Translation:Cells
    96. Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities. Biochemistry. 1993 Jun 01; 32(21):5560-5. Chakrabartty A, Kortemme T, Padmanabhan S, Baldwin RL. PMID: 8504077.
      View in: PubMed   Mentions: 52     Fields:    Translation:Cells
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