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dc.contributor.authorBorrman, Tyler M.
dc.contributor.authorCimons, Jennifer M.
dc.contributor.authorCosiano, Michael
dc.contributor.authorPurcaro, Michael
dc.contributor.authorPierce, Brian G.
dc.contributor.authorBaker, Brian M.
dc.contributor.authorWeng, Zhiping
dc.date2022-08-11T08:07:58.000
dc.date.accessioned2022-08-23T15:37:55Z
dc.date.available2022-08-23T15:37:55Z
dc.date.issued2017-05-01
dc.date.submitted2017-07-12
dc.identifier.citationProteins. 2017 May;85(5):908-916. doi: 10.1002/prot.25260. Epub 2017 Feb 16. <a href="https://doi.org/10.1002/prot.25260">Link to article on publisher's site</a>
dc.identifier.issn0887-3585 (Linking)
dc.identifier.doi10.1002/prot.25260
dc.identifier.pmid28160322
dc.identifier.urihttp://hdl.handle.net/20.500.14038/25827
dc.description.abstractThe ATLAS (Altered TCR Ligand Affinities and Structures) database (https://zlab.umassmed.edu/atlas/web/) is a manually curated repository containing the binding affinities for wild-type and mutant T cell receptors (TCRs) and their antigens, peptides presented by the major histocompatibility complex (pMHC). The database links experimentally measured binding affinities with the corresponding three dimensional (3D) structures for TCR-pMHC complexes. The user can browse and search affinities, structures, and experimental details for TCRs, peptides, and MHCs of interest. We expect this database to facilitate the development of next-generation protein design algorithms targeting TCR-pMHC interactions. ATLAS can be easily parsed using modeling software that builds protein structures for training and testing. As an example, we provide structural models for all mutant TCRs in ATLAS, built using the Rosetta program. Utilizing these structures, we report a correlation of 0.63 between experimentally measured changes in binding energies and our predicted changes.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=28160322&dopt=Abstract">Link to Article in PubMed</a>
dc.relation.urlhttps://doi.org/10.1002/prot.25260
dc.subjectBiochemistry, Biophysics, and Structural Biology
dc.subjectBioinformatics
dc.subjectComputational Biology
dc.subjectIntegrative Biology
dc.subjectSystems Biology
dc.titleATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes
dc.typeJournal Article
dc.source.journaltitleProteins
dc.source.volume85
dc.source.issue5
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/bioinformatics_pubs/119
dc.identifier.contextkey10417172
html.description.abstract<p>The ATLAS (Altered TCR Ligand Affinities and Structures) database (https://zlab.umassmed.edu/atlas/web/) is a manually curated repository containing the binding affinities for wild-type and mutant T cell receptors (TCRs) and their antigens, peptides presented by the major histocompatibility complex (pMHC). The database links experimentally measured binding affinities with the corresponding three dimensional (3D) structures for TCR-pMHC complexes. The user can browse and search affinities, structures, and experimental details for TCRs, peptides, and MHCs of interest. We expect this database to facilitate the development of next-generation protein design algorithms targeting TCR-pMHC interactions. ATLAS can be easily parsed using modeling software that builds protein structures for training and testing. As an example, we provide structural models for all mutant TCRs in ATLAS, built using the Rosetta program. Utilizing these structures, we report a correlation of 0.63 between experimentally measured changes in binding energies and our predicted changes.</p>
dc.identifier.submissionpathbioinformatics_pubs/119
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology
dc.source.pages908-916


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