{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T17:53:05Z","timestamp":1781545985064,"version":"3.54.5"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T00:00:00Z","timestamp":1781481600000},"content-version":"vor","delay-in-days":45,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The T cell\u2019s ability to discern self and non-self depends on its T cell receptor (TCR), which recognizes peptides presented by major histocompatibility complexes (MHC) molecules. Understanding this TCR-peptide\u2013MHC (TCRpMHC) interaction is important for cancer immunotherapy design, tissue transplantation, pathogen identification, and autoimmune disease treatments. Understanding the intricacies of TCR recognition, encapsulated in TCRpMHC structures, remains challenging due to the immense diversity of TCRs (&amp;gt;108\/individual), rendering experimental determination, and general-purpose computational docking impractical. Addressing this gap, we have developed a rapid integrative modeling protocol leveraging unique docking patterns in TCRpMHC complexes. Built upon PIPER, our pipeline significantly cuts down Fast Fourier Transform rotation sets, exploiting the consistent polarized docking angle of TCRs at pMHC. Additionally, our ultra-fast structure superimposition tool, GradPose, accelerates clustering. It models a case in 3\u20134\u00a0min on 12 Central Processing Units (CPUs), showcasing a speedup of up to 25\u201340 times compared to the ClusPro webserver. On a benchmark set of 38 TCRpMHC class I (TCRpMHC-I) complexes, our protocol outperforms the state-of-the-art docking tools in model quality. This protocol can potentially provide structural information to TCR repertoires targeting specific peptides. Its computational efficiency can also enrich existing pMHC-specific single-cell sequencing TCR data, facilitating the development of structure-based deep learning algorithms. These insights are essential for understanding T cell recognition and specificity, advancing the development of therapeutic interventions.<\/jats:p>","DOI":"10.1093\/bib\/bbag306","type":"journal-article","created":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T11:49:07Z","timestamp":1780055347000},"source":"Crossref","is-referenced-by-count":0,"title":["SwiftTCR: efficient computational docking protocol of TCRpMHC-I complexes using restricted rotation matrices"],"prefix":"10.1093","volume":"27","author":[{"given":"Farzaneh M","family":"Parizi","sequence":"first","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the Netherlands"]},{"name":"Institute for Computing and Information Sciences, Radboud University , Postbus 9102, 6500 HC, Nijmegen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yannick J M","family":"Aarts","sequence":"additional","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the Netherlands"]},{"name":"Adaptation Physiology Group, Department of Animal Sciences, Wageningen University and Research , P.O. Box 9101, 6700 HB, Wageningen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nils","family":"Smit","sequence":"additional","affiliation":[{"name":"HAN University of Applied Sciences , Kapittelweg 33\u201335 6503 GL, Nijmegen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A R","family":"Dona Roran","sequence":"additional","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dani\u00eblle","family":"Diepenbroek","sequence":"additional","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wieke A","family":"Kr\u00f6sschell","sequence":"additional","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the Netherlands"]},{"name":"HAN University of Applied Sciences , Kapittelweg 33\u201335 6503 GL, Nijmegen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Levin","family":"Thijs","sequence":"additional","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joost","family":"Tepperik","sequence":"additional","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dario F","family":"Marzella","sequence":"additional","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gayatri","family":"Ramakrishnan","sequence":"additional","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2613-538X","authenticated-orcid":false,"given":"Li C","family":"Xue","sequence":"additional","affiliation":[{"name":"Medical BioSciences, Radboud University Medical Center , Geert Grooteplein Zuid 10, 6525 GA, Nijmegen ,","place":["the 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