{"links":{},"id":2008119,"metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:02008119","sets":["1164:5352:1772177578196:1772177778740"]},"path":["1772177778740"],"owner":"80578","recid":"2008119","title":["Inverse MSMD法による化合物部分構造プロファイリングと結合親和性推定"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2026-03-05"},"_buckets":{"deposit":"75bb7ed2-3dba-49a1-8a3d-4d2d9d2ccb9a"},"_deposit":{"id":"2008119","pid":{"type":"depid","value":"2008119","revision_id":0},"owners":[80578],"status":"published","created_by":80578},"item_title":"Inverse MSMD法による化合物部分構造プロファイリングと結合親和性推定","author_link":[],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Inverse MSMD法による化合物部分構造プロファイリングと結合親和性推定","subitem_title_language":"ja"},{"subitem_title":"Compound Substructure Profiling by Inverse MSMD and Its Application to Binding Affinity Prediction","subitem_title_language":"en"}]},"item_type_id":"4","publish_date":"2026-03-05","item_4_text_3":{"attribute_name":"著者所属","attribute_value_mlt":[{"subitem_text_value":"東京科学大学情報理工学院／東京科学大学中分子IT創薬研究推進体"},{"subitem_text_value":"筑波大学医学医療系／筑波大学トランスボーダー医学研究センター"},{"subitem_text_value":"筑波大学大学院理工情報生命学術院数理物質科学研究群"},{"subitem_text_value":"筑波大学医学医療系／筑波大学トランスボーダー医学研究センター"}]},"item_4_text_4":{"attribute_name":"著者所属(英)","attribute_value_mlt":[{"subitem_text_value":"School of Computing, Institute of Science Tokyo / Middle Molecule IT-based Drug Discovery Laboratory, Institute of Science Tokyo","subitem_text_language":"en"},{"subitem_text_value":"Faculty of Medicine, University of Tsukuba / Transborder Medical Research Center, University of Tsukuba","subitem_text_language":"en"},{"subitem_text_value":"Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba","subitem_text_language":"en"},{"subitem_text_value":"Faculty of Medicine, University of Tsukuba / Transborder Medical Research Center, University of Tsukuba","subitem_text_language":"en"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"jpn"}]},"item_publisher":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"情報処理学会","subitem_publisher_language":"ja"}]},"publish_status":"0","weko_shared_id":-1,"item_file_price":{"attribute_name":"Billing file","attribute_type":"file","attribute_value_mlt":[{"url":{"url":"https://ipsj.ixsq.nii.ac.jp/record/2008119/files/IPSJ-BIO26084019.pdf","label":"IPSJ-BIO26084019.pdf"},"date":[{"dateType":"Available","dateValue":"2028-03-05"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-BIO26084019.pdf","filesize":[{"value":"10.5 MB"}],"mimetype":"application/pdf","priceinfo":[{"tax":["include_tax"],"price":"660","billingrole":"5"},{"tax":["include_tax"],"price":"330","billingrole":"6"},{"tax":["include_tax"],"price":"0","billingrole":"41"},{"tax":["include_tax"],"price":"0","billingrole":"44"}],"accessrole":"open_date","version_id":"93c8832d-f41a-41c9-ba67-58db2ae0b384","displaytype":"detail","licensetype":"license_note","license_note":"Copyright (c) 2026 by the Information Processing Society of Japan"}]},"item_4_creator_5":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"柳澤,渓甫"}]},{"creatorNames":[{"creatorName":"吉野,龍ノ介"}]},{"creatorNames":[{"creatorName":"工藤,玄己"}]},{"creatorNames":[{"creatorName":"広川,貴次"}]}]},"item_4_creator_6":{"attribute_name":"著者名(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Keisuke Yanagisawa","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Ryunosuke Yoshino","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Genki Kudo","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Takatsugu Hirokawa","creatorNameLang":"en"}]}]},"item_4_source_id_9":{"attribute_name":"書誌レコードID","attribute_value_mlt":[{"subitem_source_identifier":"AA12055912","subitem_source_identifier_type":"NCID"}]},"item_4_textarea_12":{"attribute_name":"Notice","attribute_value_mlt":[{"subitem_textarea_value":"SIG Technical Reports are nonrefereed and hence may later appear in any journals, conferences, symposia, etc."}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourceuri":"http://purl.org/coar/resource_type/c_18gh","resourcetype":"technical report"}]},"item_4_source_id_11":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"2188-8590","subitem_source_identifier_type":"ISSN"}]},"item_4_description_7":{"attribute_name":"論文抄録","attribute_value_mlt":[{"subitem_description":"共溶媒分子動力学(MSMD)法は，溶媒として水分子に加えて化合物部分構造サイズの有機溶媒（プローブ）を導入した分子動力学シミュレーションを行い，タンパク質表面のどこにプローブが滞留しやすいかという情報から，タンパク質表面のホットスポット解析などを行う手法である．本研究では，このアプローチを逆転させ，プローブ表面のどこにアミノ酸残基が出現しやすいかを解析するinverse MSMD法を提案する．Inverse MSMDでは，シミュレーション中のプローブ分子周辺のタンパク質残基位置を全スナップショットにわたって記録し，その存在確率を空間的に求めることで，タンパク質残基との相互作用のプロファイルを作成する．さらに，このプロファイルを結合親和性推定に応用し，化合物の部分構造置換による結合親和性の変化を評価する．MCL-1およびTYK2を標的とした評価実験において，実験値との相関係数r = 0.50-0.59の値を得た．","subitem_description_type":"Other"}]},"item_4_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"The mixed-solvent molecular dynamics (MSMD) method performs molecular dynamics simulations by introducing substructure-sized small organic molecules (probes) together with water molecules as solvents. Based on the spatial preferences of these probes on protein surfaces, the method enables hotspot analysis. In this study, we propose an inverse MSMD method that reverses this approach by analyzing where amino acid residues tend to appear around the probe surface. In inverse MSMD, the positions of protein residues surrounding each probe molecule are accumulated across all snapshots during the simulation, and the spatial occupancy are computed to construct an interaction profile with protein residues. Furthermore, we apply this profile to binding affinity prediction and evaluate changes in binding affinity upon substructure substitution of compounds. In evaluation experiments targeting MCL-1 and TYK2, we obtained correlation coefficients of r = 0.50-0.59 with experimental values.","subitem_description_type":"Other"}]},"item_4_biblio_info_10":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicPageEnd":"8","bibliographic_titles":[{"bibliographic_title":"研究報告バイオ情報学（BIO）"}],"bibliographicPageStart":"1","bibliographicIssueDates":{"bibliographicIssueDate":"2026-03-05","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"19","bibliographicVolumeNumber":"2026-BIO-84"}]},"relation_version_is_last":true,"weko_creator_id":"80578"},"created":"2026-02-27T07:47:31.729357+00:00","updated":"2026-02-27T07:47:35.923506+00:00"}