{"created":"2025-02-21T03:56:58.743163+00:00","id":2007596,"links":{},"metadata":{"_buckets":{"deposit":"37b4e8e9-d7f4-44e2-af46-821ae962e8c4"},"_deposit":{"created_by":41,"id":"2007596","owners":[41],"pid":{"revision_id":0,"type":"depid","value":"2007596"},"status":"published"},"_oai":{"id":"oai:hiroshima.repo.nii.ac.jp:02007596","sets":["1730444907710"]},"author_link":[],"item_1617186331708":{"attribute_name":"Title","attribute_value_mlt":[{"subitem_title":"Secondary-structure design of proteins by a backbone torsion energy","subitem_title_language":"en"}]},"item_1617186419668":{"attribute_name":"Creator","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Sakae, Yoshitake","creatorNameLang":"en"}],"familyNames":[{"familyName":"Sakae","familyNameLang":"en"}],"givenNames":[{"givenName":"Yoshitake","givenNameLang":"en"}]},{"creatorNames":[{"creatorName":"Okamoto, Yuko","creatorNameLang":"en"}],"familyNames":[{"familyName":"Okamoto","familyNameLang":"en"}],"givenNames":[{"givenName":"Yuko","givenNameLang":"en"}]}]},"item_1617186476635":{"attribute_name":"Access Rights","attribute_value_mlt":[{"subitem_access_right":"open access","subitem_access_right_uri":"http://purl.org/coar/access_right/c_abf2"}]},"item_1617186499011":{"attribute_name":"Rights","attribute_value_mlt":[{"subitem_rights":"Copyright (c) 2006 The Physical Society of Japan"}]},"item_1617186609386":{"attribute_name":"Subject","attribute_value_mlt":[{"subitem_subject":"protein folding","subitem_subject_scheme":"Other"},{"subitem_subject":"force field","subitem_subject_scheme":"Other"},{"subitem_subject":"torsion energy","subitem_subject_scheme":"Other"},{"subitem_subject":"simulated annealing","subitem_subject_scheme":"Other"},{"subitem_subject":"biomolecular simulation","subitem_subject_scheme":"Other"},{"subitem_subject":"420","subitem_subject_scheme":"NDC"}]},"item_1617186626617":{"attribute_name":"Description","attribute_value_mlt":[{"subitem_description":"We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles φ and ψ. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both φ and ψ can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase/decrease the α-helix-forming tendencies by lowering/raising the torsion-energy surface in the α-helix region and likewise increase/decrease the β-sheet-forming tendencies by lowering/raising the surface in the β-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming tendencies by performing folding simulations of α-helical and β-hairpin peptides.","subitem_description_language":"en"}]},"item_1617186643794":{"attribute_name":"Publisher","attribute_value_mlt":[{"subitem_publisher":"the Physical Society of Japan"}]},"item_1617186702042":{"attribute_name":"Language","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_1617186920753":{"attribute_name":"Source Identifier","attribute_value_mlt":[{"subitem_source_identifier":"AA00704814","subitem_source_identifier_type":"NCID"},{"subitem_source_identifier":"0031-9015","subitem_source_identifier_type":"ISSN"}]},"item_1617187024783":{"attribute_name":"Page Start","attribute_value_mlt":[{"subitem_start_page":"054802"}]},"item_1617187056579":{"attribute_name":"Bibliographic Information","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2006-05","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"5","bibliographicPageStart":"054802","bibliographicVolumeNumber":"75","bibliographic_titles":[{"bibliographic_title":"Journal of the Physical Society of Japan"},{"bibliographic_title":"Journal of the Physical Society of Japan"}]}]},"item_1617258105262":{"attribute_name":"Resource Type","attribute_value_mlt":[{"resourcetype":"journal article","resourceuri":"http://purl.org/coar/resource_type/c_6501"}]},"item_1617265215918":{"attribute_name":"Version Type","attribute_value_mlt":[{"subitem_version_resource":"http://purl.org/coar/version/c_b1a7d7d4d402bcce","subitem_version_type":"AO"}]},"item_1617353299429":{"attribute_name":"Relation","attribute_value_mlt":[{"subitem_relation_type_id":{"subitem_relation_type_id_text":"10.1143/JPSJ.75.054802","subitem_relation_type_select":"DOI"}},{"subitem_relation_type":"isVersionOf","subitem_relation_type_id":{"subitem_relation_type_id_text":"http://dx.doi.org/10.1143/JPSJ.75.054802","subitem_relation_type_select":"DOI"}}]},"item_1617605131499":{"attribute_name":"File","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_access","date":[{"dateType":"Available","dateValue":"2023-03-18"}],"displaytype":"simple","filename":"JPSJ_75_054802.pdf","filesize":[{"value":"13.2 MB"}],"mimetype":"application/pdf","url":{"objectType":"fulltext","url":"https://hiroshima.repo.nii.ac.jp/record/2007596/files/JPSJ_75_054802.pdf"},"version_id":"eadb449b-ee50-470b-973c-81ff8c9eb9cc"}]},"item_1732771732025":{"attribute_name":"旧ID","attribute_value":"17273"},"item_title":"Secondary-structure design of proteins by a backbone torsion energy","item_type_id":"40003","owner":"41","path":["1730444907710"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2023-03-18"},"publish_date":"2023-03-18","publish_status":"0","recid":"2007596","relation_version_is_last":true,"title":["Secondary-structure design of proteins by a backbone torsion energy"],"weko_creator_id":"41","weko_shared_id":-1},"updated":"2025-02-21T10:15:27.317316+00:00"}