| Year |
Citation |
Score |
| 2022 |
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, ... ... Kortemme T, et al. Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. PMID 35667008 DOI: 10.1021/acs.jctc.2c00500 |
0.781 |
|
| 2022 |
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. Proceedings of the National Academy of Sciences of the United States of America. 119: e2115480119. PMID 35254891 DOI: 10.1073/pnas.2115480119 |
0.314 |
|
| 2021 |
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, ... ... Kortemme T, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7 |
0.785 |
|
| 2021 |
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. PMID 34646016 DOI: 10.1038/s41586-021-03982-6 |
0.724 |
|
| 2021 |
Verba K, Gupta M, Azumaya C, Moritz M, Pourmal S, Diallo A, Merz G, Jang G, Bouhaddou M, Fossati A, Brilot A, Diwanji D, Hernandez E, Herrera N, Kratochvil H, ... ... Kortemme T, et al. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Research Square. PMID 34031651 DOI: 10.21203/rs.3.rs-515215/v1 |
0.489 |
|
| 2021 |
Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, ... ... Kortemme T, et al. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Biorxiv : the Preprint Server For Biology. PMID 34013269 DOI: 10.1101/2021.05.10.443524 |
0.489 |
|
| 2021 |
Pan X, Kortemme T. Recent advances in de novo protein design: principles, methods, and applications. The Journal of Biological Chemistry. 100558. PMID 33744284 DOI: 10.1016/j.jbc.2021.100558 |
0.304 |
|
| 2020 |
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, ... ... Kortemme T, et al. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science (New York, N.Y.). PMID 33060197 DOI: 10.1126/science.abe9403 |
0.674 |
|
| 2020 |
Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. Expanding the space of protein geometries by computational design of de novo fold families. Science (New York, N.Y.). 369: 1132-1136. PMID 32855341 DOI: 10.1126/Science.Abc0881 |
0.394 |
|
| 2020 |
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, ... ... Kortemme T, et al. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. PMID 32645325 DOI: 10.1016/J.Cell.2020.06.034 |
0.577 |
|
| 2020 |
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, ... ... Kortemme T, et al. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. Biorxiv : the Preprint Server For Biology. PMID 32511329 DOI: 10.1101/2020.03.22.002386 |
0.665 |
|
| 2020 |
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, ... ... Kortemme T, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2 |
0.739 |
|
| 2020 |
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, ... ... Kortemme T, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/Journal.Pcbi.1007507 |
0.776 |
|
| 2020 |
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, ... ... Kortemme T, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. PMID 32353859 DOI: 10.1038/S41586-020-2286-9 |
0.684 |
|
| 2020 |
Leman JK, 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, ... ... Kortemme T, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009 |
0.739 |
|
| 2020 |
Leman JK, 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, ... ... Kortemme T, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008 |
0.753 |
|
| 2020 |
Leman JK, 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, ... ... Kortemme T, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007 |
0.741 |
|
| 2020 |
Leman JK, 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, ... ... Kortemme T, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005 |
0.728 |
|
| 2020 |
Leman JK, 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, ... ... Kortemme T, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004 |
0.737 |
|
| 2020 |
Leman JK, 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, ... ... Kortemme T, et al. Typical development workflow in the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S003 |
0.755 |
|
| 2020 |
Leman JK, 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, ... ... Kortemme T, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002 |
0.744 |
|
| 2020 |
Leman JK, 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, ... ... Kortemme T, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001 |
0.732 |
|
| 2020 |
Perry ZR, Glasgow AA, Kortemme T. Semi-explicit Solvation Improves Ligand Binding Site Design in an Allosteric Protein Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2074 |
0.33 |
|
| 2019 |
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 (New York, N.Y.). 366: 1024-1028. PMID 31754004 DOI: 10.1126/Science.Aax8780 |
0.788 |
|
| 2019 |
Loshbaugh AL, Kortemme T. Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions. Proteins. PMID 31344278 DOI: 10.1002/Prot.25790 |
0.412 |
|
| 2019 |
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. 8. PMID 31282865 DOI: 10.7554/Elife.40499 |
0.343 |
|
| 2019 |
Kundert K, Kortemme T. Computational design of structured loops for new protein functions. Biological Chemistry. 400: 275-288. PMID 30676995 DOI: 10.1515/Hsz-2018-0348 |
0.413 |
|
| 2018 |
Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas J, Heinonen M, Kortemme T. Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity Upon Mutation. The Journal of Physical Chemistry. B. PMID 29401388 DOI: 10.1021/Acs.Jpcb.7B11367 |
0.361 |
|
| 2017 |
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, ... ... Kortemme T, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125 |
0.796 |
|
| 2017 |
Alford RF, Leaver-Fay A, Jeliazkov JR, Pacella MS, Kuhlman B, Kortemme T, Gray JJ. A Deep-Dive into the Rosetta Energy Function for Biological Macromolecules Biophysical Journal. 112: 194a. DOI: 10.1016/J.Bpj.2016.11.1078 |
0.789 |
|
| 2016 |
Ritterson RS, Hoersch D, Barlow KA, Kortemme T. Design of Light-Controlled Protein Conformations and Functions. Methods in Molecular Biology (Clifton, N.J.). 1414: 197-211. PMID 27094293 DOI: 10.1007/978-1-4939-3569-7_12 |
0.792 |
|
| 2016 |
Hoersch D, Kortemme T. A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine. Structure (London, England : 1993). PMID 27021162 DOI: 10.1016/J.Str.2016.02.015 |
0.383 |
|
| 2015 |
Ollikainen N, de Jong RM, Kortemme T. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. Plos Computational Biology. 11: e1004335. PMID 26397464 DOI: 10.1371/Journal.Pcbi.1004335 |
0.773 |
|
| 2015 |
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. 10: e0130433. PMID 26335248 DOI: 10.1371/Journal.Pone.0130433 |
0.773 |
|
| 2015 |
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. Journal of Chemical Theory and Computation. 11: 609-622. PMID 25866491 DOI: 10.1021/Ct500864R |
0.78 |
|
| 2014 |
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. Proceedings of the National Academy of Sciences of the United States of America. 111: 15426-31. PMID 25313039 DOI: 10.1073/Pnas.1410624111 |
0.771 |
|
| 2014 |
Hoersch D, Roh S, Chiu W, Kortemme T. Reprogramming an ATP-Driven Biological Machine into a Light-Gated Protein Nanocage Biophysical Journal. 106: 439a. DOI: 10.1016/J.Bpj.2013.11.2472 |
0.339 |
|
| 2013 |
Hoersch D, Roh SH, Chiu W, Kortemme T. Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nature Nanotechnology. 8: 928-32. PMID 24270642 DOI: 10.1038/Nnano.2013.242 |
0.333 |
|
| 2013 |
Jackson EL, Ollikainen N, Covert AW, Kortemme T, Wilke CO. Amino-acid site variability among natural and designed proteins. Peerj. 1: e211. PMID 24255821 DOI: 10.7717/Peerj.211 |
0.764 |
|
| 2013 |
Ollikainen N, Kortemme T. Computational protein design quantifies structural constraints on amino acid covariation. Plos Computational Biology. 9: e1003313. PMID 24244128 DOI: 10.1371/Journal.Pcbi.1003313 |
0.758 |
|
| 2013 |
Ritterson RS, Kuchenbecker KM, Michalik M, Kortemme T. Design of a photoswitchable cadherin. Journal of the American Chemical Society. 135: 12516-9. PMID 23923816 DOI: 10.1021/Ja404992R |
0.783 |
|
| 2013 |
Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). Plos One. 8: e63906. PMID 23717507 DOI: 10.1371/Journal.Pone.0063906 |
0.804 |
|
| 2013 |
Stein A, Kortemme T. Improvements to robotics-inspired conformational sampling in rosetta. Plos One. 8: e63090. PMID 23704889 DOI: 10.1371/Journal.Pone.0063090 |
0.349 |
|
| 2013 |
Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, et al. Scientific benchmarks for guiding macromolecular energy function improvement. Methods in Enzymology. 523: 109-43. PMID 23422428 DOI: 10.1016/B978-0-12-394292-0.00006-0 |
0.766 |
|
| 2013 |
Ollikainen N, Smith CA, Fraser JS, Kortemme T. Flexible backbone sampling methods to model and design protein alternative conformations. Methods in Enzymology. 523: 61-85. PMID 23422426 DOI: 10.1016/B978-0-12-394292-0.00004-7 |
0.774 |
|
| 2013 |
Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJ, Jacobson MP, Kortemme T. Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure (London, England : 1993). 21: 54-64. PMID 23159126 DOI: 10.1016/J.Str.2012.10.007 |
0.339 |
|
| 2012 |
Humphris-Narayanan E, 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 Computational Biology. 8: e1002639. PMID 22927804 DOI: 10.1371/Journal.Pcbi.1002639 |
0.38 |
|
| 2012 |
Eames M, Kortemme T. Cost-benefit tradeoffs in engineered lac operons. Science (New York, N.Y.). 336: 911-5. PMID 22605776 DOI: 10.1126/Science.1219083 |
0.578 |
|
| 2012 |
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. Proceedings of the National Academy of Sciences of the United States of America. 109: 5277-82. PMID 22403064 DOI: 10.1073/Pnas.1114487109 |
0.406 |
|
| 2011 |
Chao LH, Stratton MM, Lee IH, 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: 732-45. PMID 21884935 DOI: 10.1016/J.Cell.2011.07.038 |
0.616 |
|
| 2011 |
Smith CA, Kortemme T. Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design. Plos One. 6: e20451. PMID 21789164 DOI: 10.1371/Journal.Pone.0020451 |
0.437 |
|
| 2011 |
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 Science : a Publication of the Protein Society. 20: 1082-9. PMID 21465611 DOI: 10.1002/Pro.632 |
0.697 |
|
| 2011 |
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, ... ... Kortemme T, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6 |
0.758 |
|
| 2011 |
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. Journal of Molecular Biology. 406: 215-27. PMID 21185306 DOI: 10.1016/J.Jmb.2010.12.019 |
0.577 |
|
| 2010 |
Smith CA, Kortemme T. Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. Journal of Molecular Biology. 402: 460-74. PMID 20654621 DOI: 10.1016/J.Jmb.2010.07.032 |
0.375 |
|
| 2010 |
Lauck F, Smith CA, Friedland GF, Humphris EL, Kortemme T. RosettaBackrub--a web server for flexible backbone protein structure modeling and design. Nucleic Acids Research. 38: W569-75. PMID 20462859 DOI: 10.1093/Nar/Gkq369 |
0.813 |
|
| 2010 |
Friedland GD, Kortemme T. Designing ensembles in conformational and sequence space to characterize and engineer proteins. Current Opinion in Structural Biology. 20: 377-84. PMID 20303740 DOI: 10.1016/J.Sbi.2010.02.004 |
0.8 |
|
| 2009 |
Mandell DJ, Kortemme T. Computer-aided design of functional protein interactions. Nature Chemical Biology. 5: 797-807. PMID 19841629 DOI: 10.1038/Nchembio.251 |
0.714 |
|
| 2009 |
Mandell DJ, Kortemme T. Backbone flexibility in computational protein design. Current Opinion in Biotechnology. 20: 420-8. PMID 19709874 DOI: 10.1016/J.Copbio.2009.07.006 |
0.703 |
|
| 2009 |
Mandell DJ, Coutsias EA, Kortemme T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nature Methods. 6: 551-2. PMID 19644455 DOI: 10.1038/Nmeth0809-551 |
0.624 |
|
| 2009 |
Friedland GD, Lakomek NA, 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 Computational Biology. 5: e1000393. PMID 19478996 DOI: 10.1371/Journal.Pcbi.1000393 |
0.793 |
|
| 2009 |
Oberdorf R, Kortemme T. Complex topology rather than complex membership is a determinant of protein dosage sensitivity. Molecular Systems Biology. 5: 253. PMID 19293832 DOI: 10.1038/Msb.2009.9 |
0.769 |
|
| 2009 |
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, ... ... Kortemme T, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/J.Str.2008.12.014 |
0.524 |
|
| 2009 |
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: 846-58. PMID 19194863 DOI: 10.1002/Prot.22293 |
0.332 |
|
| 2009 |
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 (London, England : 1993). 17: 41-53. PMID 19141281 DOI: 10.1016/J.Str.2008.11.004 |
0.752 |
|
| 2009 |
Ollikainen N, Sentovich E, Coelho C, Kuehlmann A, Kortemme T. SAT-based protein design Ieee/Acm International Conference On Computer-Aided Design, Digest of Technical Papers, Iccad. 128-135. |
0.743 |
|
| 2008 |
Humphris EL, Kortemme T. Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure (London, England : 1993). 16: 1777-88. PMID 19081054 DOI: 10.1016/J.Str.2008.09.012 |
0.812 |
|
| 2008 |
Friedland GD, Linares AJ, Smith CA, Kortemme T. A simple model of backbone flexibility improves modeling of side-chain conformational variability. Journal of Molecular Biology. 380: 757-74. PMID 18547586 DOI: 10.1016/J.Jmb.2008.05.006 |
0.803 |
|
| 2008 |
Smith CA, Kortemme T. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. Journal of Molecular Biology. 380: 742-56. PMID 18547585 DOI: 10.1016/J.Jmb.2008.05.023 |
0.392 |
|
| 2008 |
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 alphabeta TCR. Journal of Molecular Biology. 375: 1306-19. PMID 18155234 DOI: 10.1016/J.Jmb.2007.11.020 |
0.374 |
|
| 2007 |
Eames M, Kortemme T. Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. Structure (London, England : 1993). 15: 1442-51. PMID 17997970 DOI: 10.1016/J.Str.2007.09.010 |
0.614 |
|
| 2007 |
Humphris EL, Kortemme T. Design of multi-specificity in protein interfaces. Plos Computational Biology. 3: e164. PMID 17722975 DOI: 10.1371/Journal.Pcbi.0030164 |
0.798 |
|
| 2007 |
Lengyel CS, 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. The Journal of Biological Chemistry. 282: 30658-66. PMID 17690100 DOI: 10.1074/Jbc.M704513200 |
0.4 |
|
| 2006 |
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. Proceedings of the National Academy of Sciences of the United States of America. 103: 16692-7. PMID 17075039 DOI: 10.1073/Pnas.0608127103 |
0.751 |
|
| 2006 |
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. Proceedings of the National Academy of Sciences of the United States of America. 103: 11503-8. PMID 16864794 DOI: 10.1073/Pnas.0600489103 |
0.319 |
|
| 2006 |
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. Journal of Molecular Biology. 361: 195-208. PMID 16831445 DOI: 10.1016/J.Jmb.2006.05.022 |
0.74 |
|
| 2006 |
Palmer AE, Giacomello M, Kortemme T, Hires SA, Lev-Ram V, Baker D, Tsien RY. Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chemistry & Biology. 13: 521-30. PMID 16720273 DOI: 10.1016/J.Chembiol.2006.03.007 |
0.375 |
|
| 2006 |
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. The Journal of Biological Chemistry. 281: 5042-9. PMID 16354667 DOI: 10.1074/Jbc.M510454200 |
0.409 |
|
| 2005 |
Morozov AV, Kortemme T. Potential functions for hydrogen bonds in protein structure prediction and design. Advances in Protein Chemistry. 72: 1-38. PMID 16581371 DOI: 10.1016/S0065-3233(05)72001-5 |
0.546 |
|
| 2005 |
Jiang L, Kuhlman B, Kortemme T, Baker D. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 58: 893-904. PMID 15651050 DOI: 10.1002/Prot.20347 |
0.687 |
|
| 2004 |
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 Research. 32: 5147-62. PMID 15459285 DOI: 10.1093/Nar/Gkh785 |
0.438 |
|
| 2004 |
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. Proceedings of the National Academy of Sciences of the United States of America. 101: 6946-51. PMID 15118103 DOI: 10.1073/Pnas.0307578101 |
0.593 |
|
| 2004 |
Kortemme T, Baker D. Computational design of protein-protein interactions. Current Opinion in Chemical Biology. 8: 91-7. PMID 15036162 DOI: 10.1016/J.Cbpa.2003.12.008 |
0.504 |
|
| 2004 |
Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D. Computational redesign of protein-protein interaction specificity. Nature Structural & Molecular Biology. 11: 371-9. PMID 15034550 DOI: 10.1038/Nsmb749 |
0.745 |
|
| 2004 |
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 kappa light chain. Biochemistry. 43: 2445-57. PMID 14992582 DOI: 10.1021/Bi034873S |
0.697 |
|
| 2004 |
Kortemme T, Kim DE, Baker D. Computational alanine scanning of protein-protein interfaces. Science's Stke : Signal Transduction Knowledge Environment. 2004: pl2. PMID 14872095 DOI: 10.1126/Stke.2192004Pl2 |
0.5 |
|
| 2003 |
Boulanger MJ, Bankovich AJ, Kortemme T, Baker D, Garcia KC. Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130. Molecular Cell. 12: 577-89. PMID 14527405 DOI: 10.1016/S1097-2765(03)00365-4 |
0.359 |
|
| 2003 |
Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins. 52: 118-22. PMID 12784377 DOI: 10.1002/Prot.10384 |
0.782 |
|
| 2003 |
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 (London, England : 1993). 11: 411-22. PMID 12679019 DOI: 10.1016/S0969-2126(03)00047-9 |
0.38 |
|
| 2003 |
Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. Journal of Molecular Biology. 326: 1239-59. PMID 12589766 DOI: 10.1016/S0022-2836(03)00021-4 |
0.635 |
|
| 2003 |
Morozov AV, Kortemme T, Baker D. Evaluation of models of electrostatic interactions in proteins Journal of Physical Chemistry B. 107: 2075-2090. DOI: 10.1021/Jp0267555 |
0.607 |
|
| 2002 |
Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. Design, activity, and structure of a highly specific artificial endonuclease. Molecular Cell. 10: 895-905. PMID 12419232 DOI: 10.1016/S1097-2765(02)00690-1 |
0.461 |
|
| 2002 |
Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proceedings of the National Academy of Sciences of the United States of America. 99: 14116-21. PMID 12381794 DOI: 10.1073/Pnas.202485799 |
0.495 |
|
| 2002 |
Alm E, Morozov AV, Kortemme T, Baker D. Simple physical models connect theory and experiment in protein folding kinetics. Journal of Molecular Biology. 322: 463-76. PMID 12217703 DOI: 10.1016/S0022-2836(02)00706-4 |
0.72 |
|
| 2001 |
Convery M, Dennis C, Rowsell S, Kortemme T, Schueler-Furman O, Watters A, Engel A, Fiser A, Parkinson G, Copley R, Gilardi G, Newman R, Sinning I, Flitsch SL, Lowden PA, et al. Paper alert: Structural biology Current Opinion in Structural Biology. 11: 501-510. DOI: 10.1016/S0959-440X(00)00240-2 |
0.567 |
|
| 2000 |
Kortemme T, Kelly MJ, Kay LE, Forman-Kay J, Serrano L. Similarities between the spectrin SH3 domain denatured state and its folding transition state. Journal of Molecular Biology. 297: 1217-29. PMID 10764585 DOI: 10.1006/Jmbi.2000.3618 |
0.487 |
|
| 1999 |
Lacroix E, Kortemme T, Lopez de la Paz M, Serrano L. The design of linear peptides that fold as monomeric beta-sheet structures. Current Opinion in Structural Biology. 9: 487-93. PMID 10449370 DOI: 10.1016/S0959-440X(99)80069-4 |
0.532 |
|
| 1999 |
Ramírez-Alvarado M, Kortemme T, Blanco FJ, Serrano L. Beta-hairpin and beta-sheet formation in designed linear peptides. Bioorganic & Medicinal Chemistry. 7: 93-103. PMID 10199660 DOI: 10.1016/S0968-0896(98)00215-6 |
0.653 |
|
| 1998 |
Kortemme T, Ramírez-Alvarado M, Serrano L. Design of a 20-amino acid, three-stranded beta-sheet protein. Science (New York, N.Y.). 281: 253-6. PMID 9657719 DOI: 10.1126/Science.281.5374.253 |
0.666 |
|
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