{"id":2008126,"created":"2026-02-27T07:47:50.778527+00:00","metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:02008126","sets":["1164:5352:1772177578196:1772177778740"]},"path":["1772177778740"],"owner":"80578","recid":"2008126","title":["REST/REUS分子動力学法のパラメータ自動調整手法の開発"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2026-03-05"},"_buckets":{"deposit":"06301b60-4004-4fcd-8d08-14a37f496db0"},"_deposit":{"id":"2008126","pid":{"type":"depid","value":"2008126","revision_id":0},"owners":[80578],"status":"published","created_by":80578},"item_title":"REST/REUS分子動力学法のパラメータ自動調整手法の開発","author_link":[],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"REST/REUS分子動力学法のパラメータ自動調整手法の開発","subitem_title_language":"ja"},{"subitem_title":"Development of an Automatic Parameter Tuning Method for REST/REUS Molecular Dynamics","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情報工学系"},{"subitem_text_value":"東京科学大学情報理工学院情報工学系／東京科学大学中分子IT創薬研究推進体"},{"subitem_text_value":"東京科学大学情報理工学院情報工学系／東京科学大学中分子IT創薬研究推進体"},{"subitem_text_value":"東京科学大学情報理工学院情報工学系／東京科学大学中分子IT創薬研究推進体"}]},"item_4_text_4":{"attribute_name":"著者所属(英)","attribute_value_mlt":[{"subitem_text_value":"Department of Computer Science, School of Computing, Institute of Science Tokyo","subitem_text_language":"en"},{"subitem_text_value":"Department of Computer Science, 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":"Department of Computer Science, 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":"Department of Computer Science, School of Computing, Institute of Science Tokyo / Middle Molecule IT-based Drug Discovery Laboratory, Institute of Science Tokyo","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/2008126/files/IPSJ-BIO26084026.pdf","label":"IPSJ-BIO26084026.pdf"},"date":[{"dateType":"Available","dateValue":"2028-03-05"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-BIO26084026.pdf","filesize":[{"value":"2.1 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":"d1a799cc-e928-42b7-bfac-c8a6024311a5","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":"清水,正浩"}]},{"creatorNames":[{"creatorName":"杉田,昌岳"}]},{"creatorNames":[{"creatorName":"柳澤,渓甫"}]},{"creatorNames":[{"creatorName":"秋山,泰"}]}]},"item_4_creator_6":{"attribute_name":"著者名(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Masahiro Shimizu","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Masatake Sugita","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Keisuke Yanagisawa","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Yutaka Akiyama","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":"分子動力学（Molecular Dynamics, MD）シミュレーションは，複雑な分子の挙動を原子レベルを明らかにすることができる一方，高いエネルギー障壁によるサンプリング不足が生じやすい．この問題に対し，REST法とREUS法を組み合わせたREST/REUS法は有効であるが，レプリカ数や溶質温度集合T，拘束中心位置および拘束の強さの集合Uなど調整すべきパラメータが多く，手動調整は困難である．そこで本研究では，短時間のREST/REUS MDから得られるスナップショットのポテンシャルエネルギーとPMFに基づいて，隣接レプリカ間の交換確率が目標交換確率に近づくようNT, NU, T, Uを反復的に更新する自動調整手法を開発した．環状ペプチドB03，B08，B09の膜透過過程予測に適用した結果，production runにおける交換確率の平均絶対誤差はREST法においては平均1.98%pt，REUS法においては平均2.13%ptとなり，実用的精度で目標交換確率へ調整できた．","subitem_description_type":"Other"}]},"item_4_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"Molecular dynamics (MD) simulations can elucidate the behavior of complex molecules at the atomic level; however, they are prone to insufficient sampling due to high energy barriers. To address this issue, the combined REST/REUS method, which integrates replica exchange with solute tempering (REST) and replica exchange umbrella sampling (REUS), is effective. Nevertheless, REST/REUS involves many parameters that must be tuned―such as the numbers of replicas, the solute temperature set T, and the set U of restraint center positions and force constants―making manual tuning difficult. In this study, we developed an automated tuning method that iteratively updates NT, NU, T, and U based on the potential energies and the potential of mean force (PMF) obtained from short REST/REUS MD simulations, so that the exchange probabilities between adjacent replicas approach a target exchange probability. When applied to predicting the membrane permeation processes of cyclic peptides B03, B08, and B09, the method achieved practical accuracy in tuning toward the target exchange probability: in the production run, the mean absolute error of the exchange probability was 1.98%pt on average for REST and 2.13%pt on average for REUS.","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":"26","bibliographicVolumeNumber":"2026-BIO-84"}]},"relation_version_is_last":true,"weko_creator_id":"80578"},"updated":"2026-02-27T07:47:55.477052+00:00","links":{}}