{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:07:50Z","timestamp":1772136470205,"version":"3.50.1"},"reference-count":57,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T00:00:00Z","timestamp":1621814400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T00:00:00Z","timestamp":1621814400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-2019745"],"award-info":[{"award-number":["PHY-2019745"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-2019745"],"award-info":[{"award-number":["PHY-2019745"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-2019745"],"award-info":[{"award-number":["PHY-2019745"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-2019745"],"award-info":[{"award-number":["PHY-2019745"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-2019745"],"award-info":[{"award-number":["PHY-2019745"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-2019745"],"award-info":[{"award-number":["PHY-2019745"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-2019745"],"award-info":[{"award-number":["PHY-2019745"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-1935762"],"award-info":[{"award-number":["PHY-1935762"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"U.S. Department of Health & Human Services | NIH | National Cancer Institute","doi-asserted-by":"publisher","award":["F30CA213878"],"award-info":[{"award-number":["F30CA213878"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"publisher","award":["C-1792"],"award-info":[{"award-number":["C-1792"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004917","name":"Cancer Prevention and Research Institute of Texas","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Comput Sci"],"DOI":"10.1038\/s43588-021-00076-1","type":"journal-article","created":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T12:03:06Z","timestamp":1621857786000},"page":"362-373","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":51,"title":["Rapid assessment of T-cell receptor specificity of the immune repertoire"],"prefix":"10.1038","volume":"1","author":[{"given":"Xingcheng","family":"Lin","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8248-2888","authenticated-orcid":false,"given":"Jason T.","family":"George","sequence":"additional","affiliation":[]},{"given":"Nicholas P.","family":"Schafer","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0764-9991","authenticated-orcid":false,"given":"Kevin","family":"Ng Chau","sequence":"additional","affiliation":[]},{"given":"Michael E.","family":"Birnbaum","sequence":"additional","affiliation":[]},{"given":"Cecilia","family":"Clementi","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9448-0388","authenticated-orcid":false,"given":"Jos\u00e9 N.","family":"Onuchic","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8819-9055","authenticated-orcid":false,"given":"Herbert","family":"Levine","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,5,24]]},"reference":[{"key":"76_CR1","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.1126\/science.342.6165.1432","volume":"342","author":"J Couzin-Frankel","year":"2013","unstructured":"Couzin-Frankel, J. Cancer immunotherapy. Science 342, 1432\u20131433 (2013).","journal-title":"Science"},{"key":"76_CR2","doi-asserted-by":"publisher","first-page":"1734","DOI":"10.1126\/science.271.5256.1734","volume":"271","author":"DR Leach","year":"1996","unstructured":"Leach, D. R., Krummel, M. F. & Allison, J. P. Enhancement of antitumor immunity by CTLA-4 blockade. Science 271, 1734\u20131736 (1996).","journal-title":"Science"},{"key":"76_CR3","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1038\/nature22991","volume":"547","author":"PA Ott","year":"2017","unstructured":"Ott, P. A. et al. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 547, 217\u2013221 (2017).","journal-title":"Nature"},{"key":"76_CR4","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1097\/00062752-200211000-00006","volume":"9","author":"JJ Molldrem","year":"2002","unstructured":"Molldrem, J. J., Komanduri, K. & Wieder, E. Overexpressed differentiation antigens as targets of graft-versus-leukemia reactions. Curr. Opin. Hematol. 9, 503\u2013508 (2002).","journal-title":"Curr. Opin. Hematol."},{"key":"76_CR5","unstructured":"Abbas, A. K., Lichtman, A. H. & Pillai, S. Cellular and Molecular Immunology (Elsevier, 2018)."},{"key":"76_CR6","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1098\/rspb.1993.0062","volume":"252","author":"RJ De Boer","year":"1993","unstructured":"De Boer, R. J. & Perelson, A. S. How diverse should the immune system be? Proc. Biol. Sci. 252, 171\u2013175 (1993).","journal-title":"Proc. Biol. Sci."},{"key":"76_CR7","doi-asserted-by":"crossref","unstructured":"Yates, A. J. Theories and quantification of thymic selection. Front. Immunol. 5, 13 (2014).","DOI":"10.3389\/fimmu.2014.00013"},{"key":"76_CR8","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1016\/0092-8674(94)90331-X","volume":"76","author":"GJ Nossal","year":"1994","unstructured":"Nossal, G. J. Negative selection of lymphocytes. Cell 76, 229\u2013239 (1994).","journal-title":"Cell"},{"key":"76_CR9","doi-asserted-by":"publisher","first-page":"16671","DOI":"10.1073\/pnas.0808081105","volume":"105","author":"A Kosmrlj","year":"2008","unstructured":"Kosmrlj, A., Jha, A. K., Huseby, E. S., Kardar, M. & Chakraborty, A. K. How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proc. Natl Acad. Sci. USA 105, 16671\u201316676 (2008).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"76_CR10","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1016\/j.immuni.2015.11.002","volume":"43","author":"MM Davis","year":"2015","unstructured":"Davis, M. M. Not-so-negative selection. Immunity 43, 833\u2013835 (2015).","journal-title":"Immunity"},{"key":"76_CR11","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1006\/jtbi.1999.1003","volume":"200","author":"V Detours","year":"1999","unstructured":"Detours, V., Mehr, R. & Perelson, A. S. A quantitative theory of affinity-driven T cell repertoire selection. J. Theor. Biol. 200, 389\u2013403 (1999).","journal-title":"J. Theor. Biol."},{"key":"76_CR12","doi-asserted-by":"publisher","first-page":"E7875","DOI":"10.1073\/pnas.1708573114","volume":"114","author":"JT George","year":"2017","unstructured":"George, J. T., Kessler, D. A. & Levine, H. Effects of thymic selection on T cell recognition of foreign and tumor antigenic peptides. Proc. Natl Acad. Sci. USA 114, E7875\u2013E7881 (2017).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"76_CR13","doi-asserted-by":"publisher","first-page":"8815","DOI":"10.1073\/pnas.1812810116","volume":"116","author":"A Mayer","year":"2019","unstructured":"Mayer, A., Balasubramanian, V., Walczak, A. M. & Mora, T. How a well-adapting immune system remembers. Proc. Natl Acad. Sci. USA 116, 8815\u20138823 (2019).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"76_CR14","doi-asserted-by":"crossref","unstructured":"Altan-Bonnet, G., Mora, T. & Walczak, A. M. Quantitative immunology for physicists. Phys. Rep. 849, 1\u201383 (2020).","DOI":"10.1016\/j.physrep.2020.01.001"},{"key":"76_CR15","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.jtbi.2018.09.012","volume":"458","author":"JT George","year":"2018","unstructured":"George, J. T. & Levine, H. Stochastic modeling of tumor progression and immune evasion. J. Theor. Biol. 458, 148\u2013155 (2018).","journal-title":"J. Theor. Biol."},{"key":"76_CR16","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1158\/0008-5472.CAN-19-2732","volume":"80","author":"JT George","year":"2020","unstructured":"George, J. T. & Levine, H. Sustained coevolution in a stochastic model of cancer\u2013immune interaction. Cancer Res. 80, 811\u2013819 (2020).","journal-title":"Cancer Res."},{"key":"76_CR17","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1038\/s41589-018-0130-4","volume":"14","author":"TP Riley","year":"2018","unstructured":"Riley, T. P. et al. T cell receptor cross-reactivity expanded by dramatic peptide\u2013MHC adaptability. Nat. Chem. Biol. 14, 934\u2013942 (2018).","journal-title":"Nat. Chem. Biol."},{"key":"76_CR18","doi-asserted-by":"publisher","first-page":"2203","DOI":"10.4049\/jimmunol.1700744","volume":"199","author":"NK Singh","year":"2017","unstructured":"Singh, N. K. et al. Emerging concepts in TCR specificity: rationalizing and (maybe) predicting outcomes. J. Immunol. 199, 2203\u20132213 (2017).","journal-title":"J. Immunol."},{"key":"76_CR19","doi-asserted-by":"publisher","first-page":"1073","DOI":"10.1016\/j.cell.2014.03.047","volume":"157","author":"ME Birnbaum","year":"2014","unstructured":"Birnbaum, M. E. et al. Deconstructing the peptide-MHC specificity of T cell recognition. Cell 157, 1073\u20131087 (2014).","journal-title":"Cell"},{"key":"76_CR20","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1038\/nature22383","volume":"547","author":"P Dash","year":"2017","unstructured":"Dash, P. et al. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature 547, 89\u201393 (2017).","journal-title":"Nature"},{"key":"76_CR21","doi-asserted-by":"publisher","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","volume":"48","author":"B Reynisson","year":"2020","unstructured":"Reynisson, B., Alvarez, B., Paul, S., Peters, B. & Nielsen, M. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 48, W449\u2013W454 (2020).","journal-title":"Nucleic Acids Res."},{"key":"76_CR22","doi-asserted-by":"publisher","first-page":"881","DOI":"10.3390\/molecules24050881","volume":"24","author":"JR Abella","year":"2019","unstructured":"Abella, J. R., Antunes, D. A., Clementi, C. & Kavraki, L. E. APE-Gen: a fast method for generating ensembles of bound peptide-mhc conformations. Molecules 24, 881 (2019).","journal-title":"Molecules"},{"key":"76_CR23","doi-asserted-by":"publisher","first-page":"1583","DOI":"10.3389\/fimmu.2020.01583","volume":"11","author":"JR Abella","year":"2020","unstructured":"Abella, J. R., Antunes, D. A., Clementi, C. & Kavraki, L. E. Large-scale structure-based prediction of stable peptide binding to class I HLAs using random forests. Front. Immunol. 11, 1583 (2020).","journal-title":"Front. Immunol."},{"key":"76_CR24","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1038\/s41587-019-0280-2","volume":"37","author":"B Chen","year":"2019","unstructured":"Chen, B. et al. Predicting HLA class II antigen presentation through integrated deep learning. Nat. Biotechnol. 37, 1332\u20131343 (2019).","journal-title":"Nat. Biotechnol."},{"key":"76_CR25","doi-asserted-by":"publisher","unstructured":"Jurtz, V. I. et al. NetTCR: Sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/433706 (2018).","DOI":"10.1101\/433706"},{"key":"76_CR26","doi-asserted-by":"crossref","unstructured":"Springer, I., Besser, H., Tickotsky-Moskovitz, N., Dvorkin, S. & Louzoun, Y. Prediction of specific TCR-peptide binding from large dictionaries of TCR-peptide pairs. Front. Immunol. 11, 1803 (2020).","DOI":"10.3389\/fimmu.2020.01803"},{"key":"76_CR27","doi-asserted-by":"publisher","first-page":"W396","DOI":"10.1093\/nar\/gky432","volume":"46","author":"R Gowthaman","year":"2018","unstructured":"Gowthaman, R. & Pierce, B. G. TCRmodel: high resolution modeling of T cell receptors from sequence. Nucleic Acids Res. 46, W396\u2013W401 (2018).","journal-title":"Nucleic Acids Res."},{"key":"76_CR28","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1002\/pro.2181","volume":"22","author":"BG Pierce","year":"2013","unstructured":"Pierce, B. G. & Weng, Z. A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes. Protein Sci. 22, 35\u201346 (2013).","journal-title":"Protein Sci."},{"key":"76_CR29","doi-asserted-by":"publisher","first-page":"4337","DOI":"10.4049\/jimmunol.0901607","volume":"183","author":"J Ishizuka","year":"2009","unstructured":"Ishizuka, J. et al. Quantitating T cell cross-reactivity for unrelated peptide antigens. J. Immunol. 183, 4337\u20134345 (2009).","journal-title":"J. Immunol."},{"key":"76_CR30","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1006\/jmbi.2000.3693","volume":"298","author":"C Clementi","year":"2000","unstructured":"Clementi, C., Nymeyer, H. & Onuchic, J. N. Topological and energetic factors: what determines the structural details of the transition state ensemble and \u2018en-route\u2019 intermediates for protein folding? an investigation for small globular proteins. J. Mol. Biol. 298, 937\u2013953 (2000).","journal-title":"J. Mol. Biol."},{"key":"76_CR31","doi-asserted-by":"crossref","unstructured":"Wang, J. & Verkhivker, G. M. Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding. Phys. Rev. Lett. 90, 188101 (2003).","DOI":"10.1103\/PhysRevLett.90.188101"},{"key":"76_CR32","doi-asserted-by":"publisher","first-page":"7524","DOI":"10.1073\/pnas.84.21.7524","volume":"84","author":"JD Bryngelson","year":"1987","unstructured":"Bryngelson, J. D. & Wolynes, P. G. Spin glasses and the statistical mechanics of protein folding. Proc. Natl Acad. Sci. USA 84, 7524\u20137528 (1987).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"76_CR33","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1016\/S1359-0278(96)00033-8","volume":"1","author":"VI Abkevich","year":"1996","unstructured":"Abkevich, V. I., Gutin, A. M. & Shakhnovich, E. I. Improved design of stable and fast-folding model proteins. Fold. Des. 1, 221\u2013230 (1996).","journal-title":"Fold. Des."},{"key":"76_CR34","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1002\/ijch.201300145","volume":"54","author":"NP Schafer","year":"2014","unstructured":"Schafer, N. P., Kim, B. L., Zheng, W. & Wolynes, P. G. Learning to fold proteins using energy landscape theory. Isr. J. Chem. 54, 1311\u20131337 (2014).","journal-title":"Isr. J. Chem."},{"key":"76_CR35","doi-asserted-by":"publisher","first-page":"8494","DOI":"10.1021\/jp212541y","volume":"116","author":"A Davtyan","year":"2012","unstructured":"Davtyan, A. et al. AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. J. Phys. Chem. B 116, 8494\u20138503 (2012).","journal-title":"J. Phys. Chem. B"},{"key":"76_CR36","doi-asserted-by":"publisher","first-page":"198101","DOI":"10.1103\/PhysRevLett.99.198101","volume":"99","author":"J Wang","year":"2007","unstructured":"Wang, J. et al. Quantifying intrinsic specificity: a potential complement to affinity in drug screening. Phys Rev. Lett. 99, 198101 (2007).","journal-title":"Phys Rev. Lett."},{"key":"76_CR37","doi-asserted-by":"publisher","first-page":"2387","DOI":"10.1039\/c3sc50478f","volume":"4","author":"Z Yan","year":"2013","unstructured":"Yan, Z., Zheng, X., Wang, E. & Wang, J. Thermodynamic and kinetic specificities of ligand binding. Chem. Sci. 4, 2387\u20132395 (2013).","journal-title":"Chem. Sci."},{"key":"76_CR38","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1038\/s41586-019-1671-8","volume":"574","author":"E Alspach","year":"2019","unstructured":"Alspach, E. et al. MHC-II neoantigens shape tumour immunity and response to immunotherapy. Nature 574, 696\u2013701 (2019).","journal-title":"Nature"},{"key":"76_CR39","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.1158\/0008-5472.CAN-11-3722","volume":"72","author":"JC Castle","year":"2012","unstructured":"Castle, J. C. et al. Exploiting the mutanome for tumor vaccination. Cancer Res. 72, 1081\u20131091 (2012).","journal-title":"Cancer Res."},{"key":"76_CR40","doi-asserted-by":"crossref","unstructured":"Ogishi, M. & Yotsuyanagi, H. Quantitative prediction of the landscape of T cell epitope immunogenicity in sequence space. Front. Immunol. 10, 827 (2019).","DOI":"10.3389\/fimmu.2019.00827"},{"key":"76_CR41","doi-asserted-by":"publisher","first-page":"5823","DOI":"10.4049\/jimmunol.1100197","volume":"186","author":"EW Newell","year":"2011","unstructured":"Newell, E. W. et al. Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c \u2013I-Ek. J. Immunol. 186, 5823\u20135832 (2011).","journal-title":"J. Immunol."},{"key":"76_CR42","doi-asserted-by":"publisher","first-page":"9029","DOI":"10.1073\/pnas.89.19.9029","volume":"89","author":"RA Goldstein","year":"1992","unstructured":"Goldstein, R. A., Luthey-Schulten, Z. A. & Wolynes, P. G. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proc. Natl Acad. Sci. USA 89, 9029\u20139033 (1992).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"76_CR43","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1021\/ma00145a039","volume":"18","author":"S Miyazawa","year":"1985","unstructured":"Miyazawa, S. & Jernigan, R. L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18, 534\u2013552 (1985).","journal-title":"Macromolecules"},{"key":"76_CR44","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.molimm.2017.12.019","volume":"94","author":"E Lanzarotti","year":"2018","unstructured":"Lanzarotti, E., Marcatili, P. & Nielsen, M. Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring. Mol. Immunol. 94, 91\u201397 (2018).","journal-title":"Mol. Immunol."},{"key":"76_CR45","doi-asserted-by":"crossref","unstructured":"Webb, B. & Sali, A. Comparative protein structure modeling using MODELLER. Curr. Protoc. Bioinforma. 54, 5.6.1\u20135.6.37 (2016).","DOI":"10.1002\/cpbi.3"},{"key":"76_CR46","doi-asserted-by":"publisher","first-page":"E2905","DOI":"10.1073\/pnas.1304859110","volume":"110","author":"C Sinclair","year":"2013","unstructured":"Sinclair, C., Bains, I., Yates, A. J. & Seddon, B. Asymmetric thymocyte death underlies the CD4:CD8 T-cell ratio in the adaptive immune system. Proc. Natl Acad. Sci. USA 110, E2905\u2013E2914 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"76_CR47","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1016\/S0092-8674(00)81905-4","volume":"88","author":"J Zerrahn","year":"1997","unstructured":"Zerrahn, J., Held, W. & Raulet, D. H. The MHC reactivity of the T cell repertoire prior to positive and negative selection. Cell 88, 627\u2013636 (1997).","journal-title":"Cell"},{"key":"76_CR48","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1016\/j.jmb.2013.09.039","volume":"426","author":"LH Kapcha","year":"2014","unstructured":"Kapcha, L. H. & Rossky, P. J. A simple atomic-level hydrophobicity scale reveals protein interfacial structure. J. Mol. Biol. 426, 484\u2013498 (2014).","journal-title":"J. Mol. Biol."},{"key":"76_CR49","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1110\/ps.0239403","volume":"12","author":"M Nielsen","year":"2003","unstructured":"Nielsen, M. et al. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci. 12, 1007\u20131017 (2003).","journal-title":"Protein Sci."},{"key":"76_CR50","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1016\/j.trecan.2020.12.005","volume":"7","author":"JT George","year":"2021","unstructured":"George, J. T. & Levine, H. Implications of tumor\u2013immune coevolution on cancer evasion and optimized immunotherapy. Trends Cancer 7, 373\u2013383 (2021).","journal-title":"Trends Cancer"},{"key":"76_CR51","doi-asserted-by":"publisher","first-page":"3352","DOI":"10.1073\/pnas.0307851100","volume":"101","author":"GA Papoian","year":"2004","unstructured":"Papoian, G. A., Ulander, J., Eastwood, M. P., Luthey-Schulten, Z. & Wolynes, P. G. From the cover: water in protein structure prediction. Proc. Natl Acad. Sci. USA 101, 3352\u20133357 (2004).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"76_CR52","doi-asserted-by":"publisher","first-page":"2932","DOI":"10.1073\/pnas.95.6.2932","volume":"95","author":"KK Koretke","year":"1998","unstructured":"Koretke, K. K., Luthey-Schulten, Z. & Wolynes, P. G. Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. Proc. Natl Acad. Sci. USA 95, 2932\u20132937 (1998).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"76_CR53","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","volume":"28","author":"L Fu","year":"2012","unstructured":"Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150\u20133152 (2012).","journal-title":"Bioinformatics"},{"key":"76_CR54","doi-asserted-by":"publisher","first-page":"D405","DOI":"10.1093\/nar\/gku938","volume":"43","author":"R Vita","year":"2015","unstructured":"Vita, R. et al. The Immune Epitope Database (IEDB) 3.0. Nucleic Acids Res. 43, D405\u2013412 (2015).","journal-title":"Nucleic Acids Res."},{"key":"76_CR55","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33\u201338 (1996).","journal-title":"J. Mol. Graph."},{"key":"76_CR56","doi-asserted-by":"publisher","unstructured":"Lin, X. XingchengLin\/RACER v.1.0 Zenodo https:\/\/doi.org\/10.5281\/zenodo.4699821 (2021).","DOI":"10.5281\/zenodo.4699821"},{"key":"76_CR57","doi-asserted-by":"publisher","unstructured":"Lin, X. et al. Codes for rapid assessment of t-cell receptor specificity of the immune repertoire. Code Ocean https:\/\/doi.org\/10.24433\/CO.3204967.v2 (20 April 2021).","DOI":"10.24433\/CO.3204967.v2"}],"container-title":["Nature Computational Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s43588-021-00076-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43588-021-00076-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43588-021-00076-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,11]],"date-time":"2024-12-11T17:47:20Z","timestamp":1733939240000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s43588-021-00076-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,24]]},"references-count":57,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2021,5]]}},"alternative-id":["76"],"URL":"https:\/\/doi.org\/10.1038\/s43588-021-00076-1","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.04.06.028415","asserted-by":"object"}]},"ISSN":["2662-8457"],"issn-type":[{"value":"2662-8457","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,24]]},"assertion":[{"value":"16 September 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 April 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 May 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}