{"links":{},"id":2008105,"metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:02008105","sets":["1164:5352:1772177578196:1772177778740"]},"path":["1772177778740"],"owner":"80578","recid":"2008105","title":["共溶媒分子動力学法を活用したドッキング計算のスコアリングの改良によるバーチャルスクリーニング精度の向上"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2026-03-05"},"_buckets":{"deposit":"e4fea060-837d-4536-b643-b4d6a68a6b15"},"_deposit":{"id":"2008105","pid":{"type":"depid","value":"2008105","revision_id":0},"owners":[80578],"status":"published","created_by":80578},"item_title":"共溶媒分子動力学法を活用したドッキング計算のスコアリングの改良によるバーチャルスクリーニング精度の向上","author_link":[],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"共溶媒分子動力学法を活用したドッキング計算のスコアリングの改良によるバーチャルスクリーニング精度の向上","subitem_title_language":"ja"},{"subitem_title":"Enhancing virtual screening accuracy by improving scoring of docking calculations using mixed-solvent 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"},{"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/2008105/files/IPSJ-BIO26084004.pdf","label":"IPSJ-BIO26084004.pdf"},"date":[{"dateType":"Available","dateValue":"2028-03-05"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-BIO26084004.pdf","filesize":[{"value":"9.8 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":"e04585b3-713e-4eb2-b288-34019e394f13","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":"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行う際に，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グリッド自由エネルギーを計算できる．そこで本研究では，アセトアルデヒド，アセトニトリル，ホルムアミド，エタノールの4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グリッド自由エネルギーと従来のエネルギースコア関数の最小値をとることで，原子グリッドの修正を行った．結果として，9件の標的タンパク質でバーチャルスクリーニング実験を行ったところ，EF1%の平均値が6.65から7.36に改善された．","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 binding conformation with affinity, 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 grid free energy 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 four types of probe molecules, acetaldehyde, acetonitrile, formamide, and ethanol, were introduced independently, and modified the atomic grid by taking the minimum of grid free energy created for each specific atom types obtained and the conventional energy score function. As a result, virtual screening experiments conducted on nine target proteins improved the average EF1% value from 6.65 to 7.36.","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":"4","bibliographicVolumeNumber":"2026-BIO-84"}]},"relation_version_is_last":true,"weko_creator_id":"80578"},"created":"2026-02-27T07:46:55.368263+00:00","updated":"2026-02-27T07:47:01.010159+00:00"}