{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1360022305566242560.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.5194/mr-2022-22"}},{"identifier":{"@type":"DOI","@value":"10.5194/mr-4-57-2023"}},{"identifier":{"@type":"URI","@value":"https://mr.copernicus.org/articles/4/57/2023/mr-4-57-2023.pdf"}},{"identifier":{"@type":"DOI","@value":"10.3929/ethz-b-000602558"}},{"identifier":{"@type":"PMID","@value":"37904802"}},{"identifier":{"@type":"HANDLE","@value":"20.500.11850/602558"}}],"resourceType":"学術雑誌論文(journal article)","dc:title":[{"@value":"Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:p>Abstract. Peptides and proteins containing non-canonical amino acids (ncAAs) are a large and important class of biopolymers. They include non-ribosomally synthesised peptides, post-translationally modified proteins, expressed or synthesised proteins containing unnatural amino acids, and peptides and proteins that are chemically modified. Here, we describe a general procedure for generating atomic descriptions required to incorporate ncAAs within popular NMR structure determination software such as CYANA, CNS, Xplor-NIH and ARIA. This procedure is made publicly available via the existing Automated Topology Builder (ATB) server (atb.uq.edu.au) with all submitted ncAAs stored in a dedicated database. The described procedure also includes a general method for linking of sidechains of amino acids from CYANA templates. To ensure compatibility with other systems, atom names comply with IUPAC guidelines. In addition to describing the workflow, 3D models of complex natural products generated by CYANA are presented, including vancomycin. In order to demonstrate the manner in which the templates for ncAAs generated by the ATB can be used in practice we use a combination of CYANA and CNS to solve the structure of a synthetic peptide designed to disrupt Alzheimer-related protein-protein interactions. Automating the generation of structural templates for ncAAs will extend the utility of NMR spectroscopy to studies of more complex biomolecules, with applications in the rapidly growing fields of synthetic and chemical biology. The procedures we outline can also be used to standardise the creation of structural templates for any amino acid and thus have the potential to impact structural biology more generally.</jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1380022305566242571","@type":"Researcher","foaf:name":[{"@value":"Sarah Kuschert"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242562","@type":"Researcher","foaf:name":[{"@value":"Martin Stroet"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242564","@type":"Researcher","foaf:name":[{"@value":"Yanni Ka-Yan Chin"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242569","@type":"Researcher","foaf:name":[{"@value":"Anne Clair Conibear"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242563","@type":"Researcher","foaf:name":[{"@value":"Xinying Jia"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242570","@type":"Researcher","foaf:name":[{"@value":"Thomas Lee"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242560","@type":"Researcher","foaf:name":[{"@value":"Christian Reinhard Otto Bartling"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242565","@type":"Researcher","foaf:name":[{"@value":"Kristian Strømgaard"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242566","@type":"Researcher","foaf:name":[{"@value":"Peter Güntert"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242567","@type":"Researcher","foaf:name":[{"@value":"Karl Johan Rosengren"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242561","@type":"Researcher","foaf:name":[{"@value":"Alan Edward Mark"}]},{"@id":"https://cir.nii.ac.jp/crid/1380022305566242568","@type":"Researcher","foaf:name":[{"@value":"Mehdi Mobli"}]}],"publication":{"publicationIdentifier":[{"@type":"EISSN","@value":"26990016"}],"prism:publicationName":[{"@value":"Magnetic Resonance"}],"dc:publisher":[{"@value":"Copernicus GmbH"}],"prism:publicationDate":"2022-11-29","prism:volume":"4","prism:number":"1","prism:startingPage":"57","prism:endingPage":"72"},"reviewed":"false","dcterms:accessRights":"http://purl.org/coar/access_right/c_abf2","dc:rights":["https://creativecommons.org/licenses/by/4.0/"],"url":[{"@id":"https://mr.copernicus.org/articles/4/57/2023/mr-4-57-2023.pdf"}],"createdAt":"2022-11-29","modifiedAt":"2025-01-22","foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=Electricity%20and%20magnetism","dc:title":"Electricity and magnetism"},{"@id":"https://cir.nii.ac.jp/all?q=QC501-766","dc:title":"QC501-766"},{"@id":"https://cir.nii.ac.jp/all?q=540","dc:title":"540"},{"@id":"https://cir.nii.ac.jp/all?q=Research%20Article","dc:title":"Research Article"}],"project":[{"@id":"https://cir.nii.ac.jp/crid/1040014327096000896","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"23K05660"},{"@type":"JGN","@value":"JP23K05660"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23K05660/"}],"notation":[{"@language":"ja","@value":"Fully automated protein NMR assignments and structures from raw time-domain data by deep learning"}]}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360011142940927616","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Automatic atom type and bond type perception in molecular mechanical calculations"}]},{"@id":"https://cir.nii.ac.jp/crid/1360011143577068160","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Quality Control and Infiltration of Translation by Amino Acids Outside of the Genetic 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