{"links":{},"id":2005579,"metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:02005579","sets":["581:11839:11850"]},"path":["11850"],"owner":"80578","recid":"2005579","title":["蛋白質立体構造の窪みに充填した球を用いた化合物構築手法の提案"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2025-11-15"},"_buckets":{"deposit":"39d99ca0-b59f-4ea7-9b5f-0991d28cee3a"},"_deposit":{"id":"2005579","pid":{"type":"depid","value":"2005579","revision_id":0},"owner":"80578","owners":[80578],"status":"published","created_by":80578},"item_title":"蛋白質立体構造の窪みに充填した球を用いた化合物構築手法の提案","author_link":[],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"蛋白質立体構造の窪みに充填した球を用いた化合物構築手法の提案","subitem_title_language":"ja"},{"subitem_title":"Proposal of a Compound Construction Method Using Spheres Filled in the Cavity of the Protein 3D Structure Model","subitem_title_language":"en"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"[一般論文] 化合物構築，蛋白質三次元構造，球の充填，最小全域木，遺伝的アルゴリズム","subitem_subject_scheme":"Other"}]},"item_type_id":"2","publish_date":"2025-11-15","item_2_text_3":{"attribute_name":"著者所属","attribute_value_mlt":[{"subitem_text_value":"放送大学"},{"subitem_text_value":"放送大学"},{"subitem_text_value":"放送大学"}]},"item_2_text_4":{"attribute_name":"著者所属(英)","attribute_value_mlt":[{"subitem_text_value":"The Open University of Japan","subitem_text_language":"en"},{"subitem_text_value":"The Open University of Japan","subitem_text_language":"en"},{"subitem_text_value":"The Open University of Japan","subitem_text_language":"en"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"jpn"}]},"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/2005579/files/IPSJ-JNL6611006.pdf","label":"IPSJ-JNL6611006.pdf"},"date":[{"dateType":"Available","dateValue":"2027-11-15"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-JNL6611006.pdf","filesize":[{"value":"4.9 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":"8"},{"tax":["include_tax"],"price":"0","billingrole":"44"}],"accessrole":"open_date","version_id":"8ce1b586-7dba-4c40-b6d7-3559692c92c3","displaytype":"detail","licensetype":"license_note","license_note":"Copyright (c) 2025 by the Information Processing Society of Japan"}]},"item_2_creator_5":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"岩瀬,一彦"}]},{"creatorNames":[{"creatorName":"柳沼,良知"}]},{"creatorNames":[{"creatorName":"鈴木,一史"}]}]},"item_2_creator_6":{"attribute_name":"著者名(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Kazuhiko Iwase","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Yoshitomo Yaginuma","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Motofumi Suzuki","creatorNameLang":"en"}]}]},"item_2_source_id_9":{"attribute_name":"書誌レコードID","attribute_value_mlt":[{"subitem_source_identifier":"AN00116647","subitem_source_identifier_type":"NCID"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourceuri":"http://purl.org/coar/resource_type/c_6501","resourcetype":"journal article"}]},"item_2_publisher_15":{"attribute_name":"公開者","attribute_value_mlt":[{"subitem_publisher":"情報処理学会","subitem_publisher_language":"ja"}]},"item_2_source_id_11":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"1882-7764","subitem_source_identifier_type":"ISSN"}]},"item_2_description_7":{"attribute_name":"論文抄録","attribute_value_mlt":[{"subitem_description":"多大な計算リソースと計算時間そして複雑な操作手順を必要とせずに，創薬研究者がパーソナルコンピュータを利用して，蛋白質窪み表面に結合する化合物分子構造を構築する手法について提案する．蛋白質三次元構造モデルの化合物が結合する周辺5Åの窪みの分子表面に，その上部に並べた半径0.75Åの球（充填球）を落下充填させた．そして蛋白質窪み上部をいくつかの平面で塞いで充填球の衝突シミュレーションを行った．その後，充填球の半径を0.9Åと大きくして蛋白質窪みの分子表面からはみ出た球を削除，次いで充填球の半径を1.8～2.1Åとさらに大きくして蛋白質アンカー（化合物と相互作用する蛋白質アミノ酸残基の主要原子）付近を除いて窪みの分子表面からはみ出た球をさらに削除した．このようにして絞り込んだ充填球の中心を三次元最小全域木でつないで化合物の炭素骨格構造とし，次いで補完的に遺伝的アルゴリズムや強化学習を適用して環構造を再構成した．最後に蛋白質アンカーと相互作用可能な距離にある炭素原子を相互作用する原子（や結合）に変換して化合物分子構造を構築した．そして化合物の歪みの軽減を図り，安定化した蛋白質化合物複合体構造をドッキング計算から求めた．提案手法の有効性を明らかにするため評価実験を行い，ノイラミニダーゼに結合する抗インフルエンザ薬リレンザ誘導体が構築できることが明らかになった．","subitem_description_type":"Other"}]},"item_2_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"We propose a method that enables drug discovery researchers to construct molecular structures of compounds that bind to the surfaces of protein cavities. The surface area within Å of the compound-binding site in the protein three-dimensional structure model was filled by dropping spheres of radius 0.7Å arranged on the top of the cavity. The top of the cavity was then covered with several planes to simulate the collision of the spheres. After that, the radius of the spheres was set to 0.9Å and then 1.8-2.1Å to remove the spheres protruding from the surface of the cavity. The centers of the remaining spheres were connected to form the carbon skeleton of the compound using the three-dimensional minimum spanning tree, then genetic algorithms and reinforcement learning were applied in a complementary manner to reconstruct the ring structure. Finally, the carbon atoms that interact with the protein anchors were converted into interactable atoms (and bonds) to construct the compound structure. Evaluation experiments were conducted to demonstrate the effectiveness of the proposed method, and it was found to construct derivatives of the anti-influenza drug Relenza that binds to neuraminidase.","subitem_description_type":"Other"}]},"item_2_biblio_info_10":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicPageEnd":"1506","bibliographic_titles":[{"bibliographic_title":"情報処理学会論文誌"}],"bibliographicPageStart":"1497","bibliographicIssueDates":{"bibliographicIssueDate":"2025-11-15","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"11","bibliographicVolumeNumber":"66"}]},"relation_version_is_last":true,"item_2_identifier_registration":{"attribute_name":"ID登録","attribute_value_mlt":[{"subitem_identifier_reg_text":"10.20729/0002005579","subitem_identifier_reg_type":"JaLC"}]},"weko_creator_id":"80578"},"created":"2025-11-10T04:19:19.364629+00:00","updated":"2025-11-18T00:10:34.375770+00:00"}