Tanja Kortemme, PhD

Title(s)Professor, Bioengineering
SchoolSchool of Pharmacy
Address1700 4th Street, #308E
San Francisco CA 94158
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    Collapse Biography 
    Collapse Awards and Honors
    2022Chan Zuckerberg Biohub Investigator (renewed)
    2019American Institute for Medical and Biological Engineering (AIMBE) Elected Fellow
    2017Chan Zuckerberg Biohub Investigator
    2013W.M. Keck Foundation Medical Research Award
    2008National Science Foundation (NSF) Faculty Early Career Development (CAREER) Award
    2005Sloan Foundation Research Fellow
    2000Human Frontiers Science Program (HFSP) Postdoctoral Fellow
    1999European Molecular Biology Organization (EMBO) Postdoctoral Fellow
    1993European Molecular Biology Laboratory (EMBL) Graduate Fellowship
    1989German National Academic Foundation ("Studienstiftung des Deutschen Volkes") Scholarship

    Collapse Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    Quantifying molecular and cellular constraints on protein function through in vivo fitness assays and computational protein design
    NSF MCB-1615990Aug 1, 2016 - Jul 31, 2021
    Role: Principal Investigator
    Robotics-inspired modeling & design of proteins
    NSF DBI-1564692Apr 15, 2016 - Mar 31, 2020
    Role: Principal Investigator
    Discovery of Protein Network Function
    NIH/NIGMS R01GM117189Jan 1, 2016 - Dec 31, 2020
    Role: Principal Investigator
    Computational design of new protein structures and interactions
    NIH/NIGMS R01GM110089May 1, 2015 - Apr 30, 2024
    Role: Principal Investigator
    Computational design of protein-based modular small-molecule biosensors
    NIH R21EB013389Apr 1, 2011 - Mar 31, 2014
    Role: Principal Investigator
    Molecular Biophysics Training Grant
    NIH T32GM008284Sep 30, 1988 - Jun 30, 2023
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

    Collapse Featured Content 
    Collapse Twitter

    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.
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    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. An integrative approach to protein sequence design through multiobjective optimization. bioRxiv. 2024 Mar 04. Hong L, Kortemme T. PMID: 38496480; PMCID: PMC10942313.
      View in: PubMed   Mentions:
    2. Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR-T cells. bioRxiv. 2024 Feb 28. Kasap C, Izgutdina A, Patiño-Escobar B, Kang A, Chilakapati N, Akagi N, Johnson H, Rashid T, Werner J, Barpanda A, Geng H, Lin YT, Rampersaud S, Gil-Alós D, Sobh A, Dupéré-Richer D, Wicaksono G, Kawehi Kelii KM, Dalal R, Ramos E, Vijayanarayanan A, Salangsang F, Phojanakong P, Serrano JAC, Zakraoui O, Tariq I, Steri V, Shanmugam M, Boise LH, Kortemme T, Stieglitz E, Licht JD, Karlon WJ, Barwick BG, Wiita AP. PMID: 38463958; PMCID: PMC10925123.
      View in: PubMed   Mentions:
    3. De novo protein design-From new structures to programmable functions. Cell. 2024 Feb 01; 187(3):526-544. Kortemme T. PMID: 38306980; PMCID: PMC10990048.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    4. Author Correction: Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor. Nat Commun. 2023 Jul 14; 14(1):4208. Glasgow A, Hobbs HT, Perry ZR, Wells ML, Marqusee S, Kortemme T. PMID: 37452025; PMCID: PMC10349067.
      View in: PubMed   Mentions:    Fields:    
    5. Multi-input Drug-Controlled Switches of Mammalian Gene Expression Based on Engineered Nuclear Hormone Receptors. ACS Synth Biol. 2023 07 21; 12(7):1924-1934. Kretschmer S, Perry N, Zhang Y, Kortemme T. PMID: 37315218; PMCID: PMC10367131.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. Emerging maps of allosteric regulation in cellular networks. Curr Opin Struct Biol. 2023 06; 80:102602. Mathy CJP, Kortemme T. PMID: 37150039; PMCID: PMC10960510.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    7. Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor. Nat Commun. 2023 03 02; 14(1):1179. Glasgow A, Hobbs HT, Perry ZR, Wells ML, Marqusee S, Kortemme T. PMID: 36859492; PMCID: PMC9977783.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    8. A complete allosteric map of a GTPase switch in its native cellular network. Cell Syst. 2023 03 15; 14(3):237-246.e7. Mathy CJP, Mishra P, Flynn JM, Perica T, Mavor D, Bolon DNA, Kortemme T. PMID: 36801015; PMCID: PMC10173951.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    9. Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. Structure. 2023 03 02; 31(3):253-264.e6. Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech TH, 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. PMID: 36805129; PMCID: PMC9936628.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    10. Multi-input drug-controlled switches of mammalian gene expression based on engineered nuclear hormone receptors. bioRxiv. 2023 Feb 01. Kretschmer S, Perry N, Zhang Y, Kortemme T. PMID: 36778233; PMCID: PMC9915577.
      View in: PubMed   Mentions:
    11. Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. bioRxiv. 2022 Aug 10. Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech TH, Lui I, Laurie MT, Glasgow J, Le CQ, Zhang Y, Diwanji D, Hernandez E, Lopez J, 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. PMID: 35982665; PMCID: PMC9387132.
      View in: PubMed   Mentions:
    12. Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". J Chem Theory Comput. 2022 Jul 12; 18(7):4594. 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: 35667008.
      View in: PubMed   Mentions: 1     Fields:    
    13. Advances in the Computational Design of Small-Molecule-Controlled Protein-Based Circuits for Synthetic Biology. Proc IEEE Inst Electr Electron Eng. 2022 May; 110(5):659-674. Kretschmer S, Kortemme T. PMID: 36531560; PMCID: PMC9754107.
      View in: PubMed   Mentions: 3  
    14. Accurate positioning of functional residues with robotics-inspired computational protein design. Proc Natl Acad Sci U S A. 2022 03 15; 119(11):e2115480119. Krivacic C, Kundert K, Pan X, Pache RA, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, Kortemme T. PMID: 35254891; PMCID: PMC8931229.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    15. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nat Commun. 2021 11 29; 12(1):6947. 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, Ljubetic A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Ó Conchúir S, Roy Burman SS, 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. PMID: 34845212; PMCID: PMC8630030.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    16. De novo protein fold families expand the designable ligand binding site space. PLoS Comput Biol. 2021 11; 17(11):e1009620. Pan X, Kortemme T. PMID: 34807909; PMCID: PMC8648124.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    17. Systems-level effects of allosteric perturbations to a model molecular switch. Nature. 2021 11; 599(7883):152-157. Perica T, Mathy CJP, Xu J, Jang G?, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T. PMID: 34646016; PMCID: PMC8571063.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    18. Design principles of protein switches. Curr Opin Struct Biol. 2022 02; 72:71-78. Alberstein RG, Guo AB, Kortemme T. PMID: 34537489; PMCID: PMC8860883.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    19. Reply to Liu et al.: Specific mutations matter in specificity and catalysis in ACE2. Proc Natl Acad Sci U S A. 2021 04 13; 118(15). Glasgow J, Glasgow A, Kortemme T, Wells JA. PMID: 33833059; PMCID: PMC8053976.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    20. Recent advances in de novo protein design: Principles, methods, and applications. J Biol Chem. 2021 Jan-Jun; 296:100558. Pan X, Kortemme T. PMID: 33744284; PMCID: PMC8065224.
      View in: PubMed   Mentions: 54     Fields:    Translation:Cells
    21. Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. Proc Natl Acad Sci U S A. 2020 11 10; 117(45):28046-28055. 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. PMID: 33093202; PMCID: PMC7668070.
      View in: PubMed   Mentions: 140     Fields:    Translation:HumansAnimalsCells
    22. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 12 04; 370(6521). Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, et al. PMID: 33060197; PMCID: PMC7808408.
      View in: PubMed   Mentions: 338     Fields:    Translation:HumansCells
    23. New computational protein design methods for de novo small molecule binding sites. PLoS Comput Biol. 2020 10; 16(10):e1008178. Lucas JE, Kortemme T. PMID: 33017412; PMCID: PMC7575090.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    24. 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; PMCID: PMC7787817.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    25. Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme. Elife. 2020 07 23; 9. Thompson S, Zhang Y, Ingle C, Reynolds KA, Kortemme T. PMID: 32701056; PMCID: PMC7377907.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    26. 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; PMCID: PMC7321036.
      View in: PubMed   Mentions: 480     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    27. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods. 2020 07; 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; PMCID: PMC7603796.
      View in: PubMed   Mentions: 245     Fields:    Translation:Cells
    28. 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, 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. PMID: 32365137; PMCID: PMC7197760.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    29. 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; PMCID: PMC7431030.
      View in: PubMed   Mentions: 2284     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    30. 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; PMCID: PMC7343396.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    31. 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; PMCID: PMC6901717.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    32. 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; PMCID: PMC6728138.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    33. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 2019 May 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; PMCID: PMC6509140.
      View in: PubMed   Mentions: 60     Fields:    
    34. Computational design of structured loops for new protein functions. Biol Chem. 2019 02 25; 400(3):275-288. Kundert K, Kortemme T. PMID: 30676995; PMCID: PMC6530579.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    35. 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; PMCID: PMC6078352.
      View in: PubMed   Mentions: 12     Fields:    
    36. 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; PMCID: PMC5980710.
      View in: PubMed   Mentions: 93     Fields:    Translation:Cells
    37. 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; PMCID: PMC5625904.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    38. 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; PMCID: PMC5538825.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    39. 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; PMCID: PMC5717763.
      View in: PubMed   Mentions: 501     Fields:    Translation:Cells
    40. 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; PMCID: PMC4862753.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimals
    41. 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: 2     Fields:    Translation:Cells
    42. 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; PMCID: PMC5088771.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    43. 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; PMCID: PMC4580623.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    44. 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; PMCID: PMC4559433.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    45. 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; PMCID: PMC4390092.
      View in: PubMed   Mentions: 118     Fields:    Translation:Cells
    46. 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; PMCID: PMC4217408.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    47. 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:    
    48. 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; PMCID: PMC3859876.
      View in: PubMed   Mentions: 17     Fields:    
    49. Computational protein design quantifies structural constraints on amino acid covariation. PLoS Comput Biol. 2013; 9(11):e1003313. Ollikainen N, Kortemme T. PMID: 24244128; PMCID: PMC3828131.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    50. 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; PMCID: PMC3828621.
      View in: PubMed   Mentions: 8     Fields:    
    51. 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; PMCID: PMC3774674.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    52. 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; PMCID: PMC3661552.
      View in: PubMed   Mentions: 192     Fields:    Translation:Cells
    53. Improvements to robotics-inspired conformational sampling in rosetta. PLoS One. 2013; 8(5):e63090. Stein A, Kortemme T. PMID: 23704889; PMCID: PMC3660577.
      View in: PubMed   Mentions: 100     Fields:    Translation:Cells
    54. 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; PMCID: PMC3724755.
      View in: PubMed   Mentions: 115     Fields:    Translation:Cells
    55. 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; PMCID: PMC3750959.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    56. 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: 9     Fields:    Translation:HumansCells
    57. 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; PMCID: PMC3426558.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    58. 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: 48     Fields:    Translation:Cells
    59. 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; PMCID: PMC3325720.
      View in: PubMed   Mentions: 39     Fields:    Translation:AnimalsCells
    60. 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; PMCID: PMC3310911.
      View in: PubMed   Mentions: 412     Fields:    Translation:HumansCells
    61. 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; PMCID: PMC3184253.
      View in: PubMed   Mentions: 138     Fields:    Translation:HumansAnimalsCells
    62. 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; PMCID: PMC3138746.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    63. 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; PMCID: PMC3104238.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    64. 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; PMCID: PMC4083816.
      View in: PubMed   Mentions: 906     Fields:    
    65. 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; PMCID: PMC3033806.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    66. 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; PMCID: PMC2928020.
      View in: PubMed   Mentions: 152     Fields:    Translation:HumansAnimalsCells
    67. 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: 50     Fields:    Translation:Cells
    68. 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; PMCID: PMC2896185.
      View in: PubMed   Mentions: 53     Fields:    Translation:Cells
    69. 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
    70. 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: 75     Fields:    Translation:Cells
    71. 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: 51     Fields:    Translation:Cells
    72. 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; PMCID: PMC2847683.
      View in: PubMed   Mentions: 236     Fields:    Translation:Cells
    73. 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; PMCID: PMC3978785.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    74. 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; PMCID: PMC2682763.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    75. 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; PMCID: PMC2671925.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    76. 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; PMCID: PMC2739730.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansAnimalsCells
    77. 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; PMCID: PMC2654222.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    78. 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.
    79. 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: 36     Fields:    Translation:HumansCells
    80. 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; PMCID: PMC2629119.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    81. 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; PMCID: PMC2603262.
      View in: PubMed   Mentions: 150     Fields:    Translation:Cells
    82. 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; PMCID: PMC3574579.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    83. 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; PMCID: PMC2330282.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCellsPHPublic Health
    84. 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; PMCID: PMC2600897.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    85. 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
    86. Design of multi-specificity in protein interfaces. PLoS Comput Biol. 2007 Aug; 3(8):e164. Humphris EL, Kortemme T. PMID: 17722975; PMCID: PMC1950952.
      View in: PubMed   Mentions: 59     Fields:    Translation:Cells
    87. 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; PMCID: PMC1629002.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansAnimalsCells
    88. 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; PMCID: PMC1544199.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    89. 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: 69     Fields:    Translation:Cells
    90. 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: 240     Fields:    Translation:HumansCells
    91. 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; PMCID: PMC1455478.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    92. 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: 57     Fields:    Translation:Cells
    93. 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: 23     Fields:    Translation:Cells
    94. 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; PMCID: PMC521638.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    95. 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; PMCID: PMC406446.
      View in: PubMed   Mentions: 83     Fields:    Translation:Cells
    96. 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: 130     Fields:    Translation:Cells
    97. 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: 11     Fields:    Translation:HumansCells
    98. 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: 240     Fields:    Translation:Cells
    99. 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: 82     Fields:    Translation:HumansCells
    100. Evaluation of Models of Electrostatic Interactions in Proteins. J. Phys. Chem. B. 2003; 107:2075-90. Morozov AV, Kortemme T, Baker D.
    101. 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: 58     Fields:    Translation:AnimalsCells
    102. 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: 45     Fields:    Translation:Cells
    103. 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: 39     Fields:    Translation:HumansAnimalsCells
    104. 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: 198     Fields:    Translation:Cells
    105. 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; PMCID: PMC137846.
      View in: PubMed   Mentions: 341     Fields:    Translation:Cells
    106. 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
    107. 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
    108. 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: 20     Fields:    Translation:Cells
    109. 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: 26     Fields:    Translation:Cells
    110. 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: 61     Fields:    Translation:Cells
    111. 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: 93     Fields:    Translation:Cells
    112. 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: 35     Fields:    Translation:Cells
    113. 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
    114. 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: 92     Fields:    Translation:Cells
    115. 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; PMCID: PMC2142718.
      View in: PubMed   Mentions: 157     Fields:    Translation:Cells
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