{"links":{},"id":2002719,"metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:02002719","sets":["1164:5352:1740054670081:1749434252473"]},"path":["1749434252473"],"owner":"80578","recid":"2002719","title":["共溶媒分子動力学シミュレーションで得られるプローブ原子分布を活用したドッキング計算のスコアリングの改良"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2025-06-14"},"_buckets":{"deposit":"18561e6c-6090-4203-b74f-b73e05c23f90"},"_deposit":{"id":"2002719","pid":{"type":"depid","value":"2002719","revision_id":0},"owners":[80578],"status":"published","created_by":80578},"item_title":"共溶媒分子動力学シミュレーションで得られるプローブ原子分布を活用したドッキング計算のスコアリングの改良","author_link":[],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"共溶媒分子動力学シミュレーションで得られるプローブ原子分布を活用したドッキング計算のスコアリングの改良","subitem_title_language":"ja"},{"subitem_title":"Probe atom distributions obtained from mixed-solvent molecular dynamics improves scoring of docking calculations","subitem_title_language":"en"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"バイオ情報学（IPSJ-BIO）2","subitem_subject_scheme":"Other"}]},"item_type_id":"4","publish_date":"2025-06-14","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"},{"subitem_text_value":"東京科学大学情報理工学院情報工学系"}]},"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","subitem_text_language":"en"},{"subitem_text_value":"Department of Computer Science, School of Computing, 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/2002719/files/IPSJ-BIO25082043.pdf","label":"IPSJ-BIO25082043.pdf"},"date":[{"dateType":"Available","dateValue":"2027-06-14"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-BIO25082043.pdf","filesize":[{"value":"13.3 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":"bf61a4d7-305c-4675-87a9-5bded664fa97","displaytype":"detail","licensetype":"license_note","license_note":"Copyright (c) 2025 by the Information Processing Society of Japan"}]},"item_4_creator_5":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"赤木,果歩"}]},{"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":"Kaho Akaki","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":"タンパク質-化合物ドッキング計算は，標的タンパク質と化合物との結合の強さとその複合体構造を予測する手法であり，薬剤候補化合物を早期段階で選抜するバーチャルスクリーニングに活用されている．ドッキング計算では，スコアリングに用いられる原子グリッドはエネルギースコア関数に基づいて計算されるが，タンパク質の柔軟性や溶媒の影響が十分に反映されていないという問題がある．一方，共溶媒分子動力学法は，タンパク質の分子動力学シミュレーションをする際に，水に加えてプローブ分子を混ぜる手法であり，プローブ分子に含まれる特徴的な原子毎の存在確率に基づいて，タンパク質の柔軟性や溶媒の影響を加味した各自由エネルギーマップを計算できる．そこで本研究では，エタノールとピロールの2種類のプローブ分子を独立に導入したそれぞれの系で共溶媒分子動力学シミュレーションを行い，得られた特徴的な原子毎に作成した各自由エネルギーマップと従来のエネルギースコア関数の平均をとることで，原子グリッドの修正を行った．結果として，最良の条件では9件の標的タンパク質のうち5件で活性化合物のスクリーニングにおける予測精度の改善が見られた．","subitem_description_type":"Other"}]},"item_4_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"Protein-compound docking is a method for predicting the strength and the complex conformation of their binding, and is used for virtual screening of drug candidate compounds. The atomic grid used in scoring is calculated based on the energy score function, but it does not reflect the flexibility of the protein or the effect of solvents. Mixed-solvent molecular dynamics is a method of mixing small probe molecules with water in molecular dynamics simulations of proteins, and can calculate each free energy maps based on the probability of existence of each specific atom types in a probe molecule, taking into account the effects of protein flexibility and solvent. In this study, we performed simulations in each system in which two types of probe molecules, ethanol and pyrrole, were introduced independently, and modified the atomic grid by taking the average of each free energy maps created for each specific atom types obtained and the conventional energy score function. Under the best conditions, the results showed that the virtual screening accuracy was improved for five of the nine target proteins.","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":"2025-06-14","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"43","bibliographicVolumeNumber":"2025-BIO-82"}]},"relation_version_is_last":true,"weko_creator_id":"80578"},"created":"2025-06-09T02:38:37.457012+00:00","updated":"2025-10-09T02:37:00.399056+00:00"}