{"id":"https://openalex.org/W4402272925","doi":"https://doi.org/10.1021/acs.jcim.4c01169","title":"FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses","display_name":"FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses","publication_year":2024,"publication_date":"2024-09-05","ids":{"openalex":"https://openalex.org/W4402272925","doi":"https://doi.org/10.1021/acs.jcim.4c01169","pmid":"https://pubmed.ncbi.nlm.nih.gov/39235048"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01169","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01169","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01169?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01169?ref=article_openPDF","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022455636","display_name":"Hirotomo Moriwaki","orcid":"https://orcid.org/0000-0002-3122-8580"},"institutions":[{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hirotomo Moriwaki","raw_affiliation_strings":["Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3122-8580","affiliations":[{"raw_affiliation_string":"Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210116810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103219688","display_name":"Yusuke Kawashima","orcid":"https://orcid.org/0000-0001-8465-6848"},"institutions":[{"id":"https://openalex.org/I36296616","display_name":"Hoshi University","ror":"https://ror.org/01mrvbd33","country_code":"JP","type":"education","lineage":["https://openalex.org/I36296616"]},{"id":"https://openalex.org/I74894318","display_name":"Ebara (Japan)","ror":"https://ror.org/02yemx219","country_code":"JP","type":"company","lineage":["https://openalex.org/I74894318"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yusuke Kawashima","raw_affiliation_strings":["Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan"],"raw_orcid":"https://orcid.org/0000-0001-8465-6848","affiliations":[{"raw_affiliation_string":"Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan","institution_ids":["https://openalex.org/I36296616","https://openalex.org/I74894318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076104735","display_name":"Chiduru Watanabe","orcid":"https://orcid.org/0000-0002-0742-3896"},"institutions":[{"id":"https://openalex.org/I4210086780","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19","country_code":"JP","type":"government","lineage":["https://openalex.org/I4210086780"]},{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Chiduru Watanabe","raw_affiliation_strings":["Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","JST PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan"],"raw_orcid":"https://orcid.org/0000-0002-0742-3896","affiliations":[{"raw_affiliation_string":"Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210116810"]},{"raw_affiliation_string":"JST PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan","institution_ids":["https://openalex.org/I4210086780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063038781","display_name":"Kikuko Kamisaka","orcid":"https://orcid.org/0000-0002-1215-2525"},"institutions":[{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kikuko Kamisaka","raw_affiliation_strings":["Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"raw_orcid":"https://orcid.org/0000-0002-1215-2525","affiliations":[{"raw_affiliation_string":"Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210116810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084712590","display_name":"Yoshio Okiyama","orcid":"https://orcid.org/0000-0002-6775-8604"},"institutions":[{"id":"https://openalex.org/I65837984","display_name":"Kobe University","ror":"https://ror.org/03tgsfw79","country_code":"JP","type":"education","lineage":["https://openalex.org/I65837984"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshio Okiyama","raw_affiliation_strings":["Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan"],"raw_orcid":"https://orcid.org/0000-0002-6775-8604","affiliations":[{"raw_affiliation_string":"Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan","institution_ids":["https://openalex.org/I65837984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079773397","display_name":"Kaori Fukuzawa","orcid":"https://orcid.org/0000-0001-5357-8250"},"institutions":[{"id":"https://openalex.org/I36296616","display_name":"Hoshi University","ror":"https://ror.org/01mrvbd33","country_code":"JP","type":"education","lineage":["https://openalex.org/I36296616"]},{"id":"https://openalex.org/I74894318","display_name":"Ebara (Japan)","ror":"https://ror.org/02yemx219","country_code":"JP","type":"company","lineage":["https://openalex.org/I74894318"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kaori Fukuzawa","raw_affiliation_strings":["Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan","Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan"],"raw_orcid":"https://orcid.org/0000-0001-5357-8250","affiliations":[{"raw_affiliation_string":"Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan","institution_ids":["https://openalex.org/I36296616","https://openalex.org/I74894318"]},{"raw_affiliation_string":"Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054336320","display_name":"Teruki Honma","orcid":"https://orcid.org/0000-0003-3761-9504"},"institutions":[{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Teruki Honma","raw_affiliation_strings":["Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"raw_orcid":"https://orcid.org/0000-0003-3761-9504","affiliations":[{"raw_affiliation_string":"Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210116810"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5076104735"],"corresponding_institution_ids":["https://openalex.org/I4210086780","https://openalex.org/I4210116810"],"apc_list":null,"apc_paid":null,"fwci":2.2009,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.89085057,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"64","issue":"18","first_page":"6927","last_page":"6937"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9929999709129333,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.989799976348877,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fragment-molecular-orbital","display_name":"Fragment molecular orbital","score":0.8667055368423462},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.7362163066864014},{"id":"https://openalex.org/keywords/metalloprotein","display_name":"Metalloprotein","score":0.6960668563842773},{"id":"https://openalex.org/keywords/biomolecule","display_name":"Biomolecule","score":0.6950973868370056},{"id":"https://openalex.org/keywords/covalent-bond","display_name":"Covalent bond","score":0.6346498727798462},{"id":"https://openalex.org/keywords/molecular-orbital","display_name":"Molecular orbital","score":0.5866312980651855},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5013167858123779},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4861313998699188},{"id":"https://openalex.org/keywords/quantum-chemical","display_name":"Quantum chemical","score":0.4372588098049164},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.43127351999282837},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.3806631565093994},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.32540857791900635},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.30550384521484375},{"id":"https://openalex.org/keywords/metal","display_name":"Metal","score":0.1342487335205078},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10850441455841064},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09554415941238403},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.0908392071723938},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.07741689682006836}],"concepts":[{"id":"https://openalex.org/C105302883","wikidata":"https://www.wikidata.org/wiki/Q5477685","display_name":"Fragment molecular orbital","level":4,"score":0.8667055368423462},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.7362163066864014},{"id":"https://openalex.org/C17165728","wikidata":"https://www.wikidata.org/wiki/Q423350","display_name":"Metalloprotein","level":3,"score":0.6960668563842773},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.6950973868370056},{"id":"https://openalex.org/C180577832","wikidata":"https://www.wikidata.org/wiki/Q127920","display_name":"Covalent bond","level":2,"score":0.6346498727798462},{"id":"https://openalex.org/C139358910","wikidata":"https://www.wikidata.org/wiki/Q725417","display_name":"Molecular orbital","level":3,"score":0.5866312980651855},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5013167858123779},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4861313998699188},{"id":"https://openalex.org/C2991951333","wikidata":"https://www.wikidata.org/wiki/Q188403","display_name":"Quantum chemical","level":3,"score":0.4372588098049164},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.43127351999282837},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.3806631565093994},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.32540857791900635},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.30550384521484375},{"id":"https://openalex.org/C544153396","wikidata":"https://www.wikidata.org/wiki/Q11426","display_name":"Metal","level":2,"score":0.1342487335205078},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10850441455841064},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09554415941238403},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.0908392071723938},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.07741689682006836},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c01169","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01169","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01169?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39235048","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39235048","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11505893","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11505893/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11505893/pdf/ci4c01169.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c01169","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01169","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01169?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6047590619","display_name":null,"funder_award_id":"JP21am0101113","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G8221952219","display_name":null,"funder_award_id":"JPMJPR18GD","funder_id":"https://openalex.org/F4320338111","funder_display_name":"Precursory Research for Embryonic Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320335125","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98"},{"id":"https://openalex.org/F4320338111","display_name":"Precursory Research for Embryonic Science and Technology","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402272925.pdf","grobid_xml":"https://content.openalex.org/works/W4402272925.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W44795381","https://openalex.org/W1967229202","https://openalex.org/W1975723203","https://openalex.org/W1977712056","https://openalex.org/W1980717010","https://openalex.org/W1983558201","https://openalex.org/W2026606763","https://openalex.org/W2032880183","https://openalex.org/W2033302770","https://openalex.org/W2033777798","https://openalex.org/W2036203032","https://openalex.org/W2042466680","https://openalex.org/W2052070468","https://openalex.org/W2082676846","https://openalex.org/W2089351320","https://openalex.org/W2095148640","https://openalex.org/W2118622794","https://openalex.org/W2131197116","https://openalex.org/W2299845867","https://openalex.org/W2316407953","https://openalex.org/W2335367147","https://openalex.org/W2479973376","https://openalex.org/W2595024785","https://openalex.org/W2622729193","https://openalex.org/W2762262121","https://openalex.org/W2767688229","https://openalex.org/W2768986438","https://openalex.org/W2862130197","https://openalex.org/W2885950556","https://openalex.org/W2897744609","https://openalex.org/W2903536205","https://openalex.org/W2903804297","https://openalex.org/W2906690049","https://openalex.org/W2908736758","https://openalex.org/W2921268473","https://openalex.org/W2922733835","https://openalex.org/W3015095584","https://openalex.org/W3015944046","https://openalex.org/W3017260797","https://openalex.org/W3043320795","https://openalex.org/W3093043010","https://openalex.org/W3102090680","https://openalex.org/W3118391549","https://openalex.org/W3118612759","https://openalex.org/W3118698050","https://openalex.org/W3120746814","https://openalex.org/W3122608869","https://openalex.org/W3189646261","https://openalex.org/W3198913336","https://openalex.org/W4229045071","https://openalex.org/W4247067116","https://openalex.org/W4280530295","https://openalex.org/W4282916790","https://openalex.org/W4283215631","https://openalex.org/W4284962741","https://openalex.org/W4285494698","https://openalex.org/W4293069267","https://openalex.org/W4296480803","https://openalex.org/W4297053268","https://openalex.org/W4297540257","https://openalex.org/W4310565651","https://openalex.org/W4322720394","https://openalex.org/W4323532207","https://openalex.org/W4362661361","https://openalex.org/W4384028690","https://openalex.org/W4384821861"],"related_works":["https://openalex.org/W1970338871","https://openalex.org/W4384821861","https://openalex.org/W2039976623","https://openalex.org/W2002112079","https://openalex.org/W1005092109","https://openalex.org/W2051453344","https://openalex.org/W2027855324","https://openalex.org/W2010338535","https://openalex.org/W1981889004","https://openalex.org/W2024642615"],"abstract_inverted_index":{"High":[0],"Resolution":[1],"Image":[2],"Download":[3],"MS":[4],"PowerPoint":[5],"Slide":[6],"The":[7,41],"fragment":[8,44],"molecular":[9,39,149],"orbital":[10],"(FMO)":[11],"method":[12,46],"is":[13],"an":[14,48,179],"efficient":[15,180],"quantum":[16],"chemical":[17],"calculation":[18],"technique":[19],"for":[20,89,107,147,184,239],"large":[21],"biomolecules,":[22],"dividing":[23],"each":[24],"into":[25,227],"smaller":[26],"fragments":[27],"and":[28,57,67,97,124,128,156,165,181,210,242],"providing":[29],"interfragment":[30],"interaction":[31],"energies":[32],"(IFIEs)":[33],"that":[34,95],"support":[35],"our":[36,221],"understanding":[37],"of":[38,151,159,171,187],"recognition.":[40],"ab":[42],"initio":[43],"MO":[45],"(ABINIT-MP),":[47],"FMO":[49,99],"processing":[50],"program,":[51],"can":[52],"automatically":[53],"divide":[54],"typical":[55],"proteins":[56],"nucleic":[58],"acids.":[59],"In":[60,175,218],"contrast,":[61],"small":[62],"molecules":[63,241],"such":[64,83,230],"as":[65,86,231],"ligands":[66],"heterosystems":[68],"must":[69],"be":[70],"manually":[71],"divided.":[72],"Thus,":[73],"we":[74,177],"developed":[75],"a":[76,87,134],"graphical":[77],"user":[78],"interface":[79],"to":[80,195,204],"easily":[81],"handle":[82],"manual":[84,200],"fragmentation":[85,103,170,186,208,233,244],"library":[88],"the":[90,108,117,130,142,148,157,185,196,219],"Molecular":[91],"Operating":[92],"Environment":[93],"(MOE)":[94],"preprocesses":[96],"visualizes":[98],"calculations.":[100],"We":[101],"demonstrated":[102],"with":[104,153,191,206,215],"IFIE":[105,138,213],"analyses":[106],"two":[109],"following":[110],"cases:":[111],"(1)":[112],"covalent":[113],"cysteine\u2013ligand":[114],"bonding":[115],"inside":[116,133],"SARS-CoV-2":[118],"main":[119],"protease":[120],"(M":[121],"pro":[122,155],")":[123],"nirmatrelvir":[125,152],"(Paxlovid)":[126],"complex":[127],"(2)":[129],"metal":[131],"coordination":[132],"zinc-bound":[135],"cyclic":[136],"peptide.":[137],"analysis":[139,214],"successfully":[140],"identified":[141],"key":[143],"amino":[144],"acid":[145],"residues":[146],"recognition":[150],"M":[154],"details":[158],"their":[160],"interactions":[161],"(e.g.,":[162],"hydrogen":[163],"bonds":[164],"CH/\u03c0":[166],"interactions)":[167],"via":[168],"ligand":[169,232],"functional":[172],"group":[173],"units.":[174],"metalloproteins,":[176],"found":[178],"accurate":[182],"scheme":[183],"Zn":[188],"2+":[189],"ions":[190],"four":[192],"histidines":[193],"coordinated":[194],"ion.":[197],"FMOe":[198],"simplifies":[199],"fragmentation,":[201],"allowing":[202],"users":[203],"experiment":[205],"various":[207],"patterns":[209],"perform":[211],"in-depth":[212],"high":[216],"accuracy.":[217],"future,":[220],"findings":[222],"will":[223],"provide":[224],"valuable":[225],"insight":[226],"complicated":[228],"cases,":[229],"in":[234],"modality":[235],"drug":[236],"discovery,":[237],"especially":[238],"medium-sized":[240],"metalloprotein":[243],"around":[245],"metals.":[246]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}