{"id":"https://openalex.org/W2801631012","doi":"https://doi.org/10.1186/s12859-018-2073-x","title":"MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions","display_name":"MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions","publication_year":2018,"publication_date":"2018-05-01","ids":{"openalex":"https://openalex.org/W2801631012","doi":"https://doi.org/10.1186/s12859-018-2073-x","mag":"2801631012","pmid":"https://pubmed.ncbi.nlm.nih.gov/29745830"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2073-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2073-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2073-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2073-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028489710","display_name":"Takanori Hayashi","orcid":"https://orcid.org/0000-0002-5189-1865"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takanori Hayashi","raw_affiliation_strings":["Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan","Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101498880","display_name":"Yuri Matsuzaki","orcid":"https://orcid.org/0000-0002-6129-6883"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuri Matsuzaki","raw_affiliation_strings":["Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025154811","display_name":"Keisuke Yanagisawa","orcid":"https://orcid.org/0000-0003-0224-0035"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Keisuke Yanagisawa","raw_affiliation_strings":["Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan","Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061510293","display_name":"Masahito Ohue","orcid":"https://orcid.org/0000-0002-0120-1643"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]},{"id":"https://openalex.org/I4210112104","display_name":"Innovative Research (United States)","ror":"https://ror.org/01zxe4w25","country_code":"US","type":"company","lineage":["https://openalex.org/I4210112104"]},{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP","US"],"is_corresponding":true,"raw_author_name":"Masahito Ohue","raw_affiliation_strings":["AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8560, Japan. ohue@c.titech.ac.jp","Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan. ohue@c.titech.ac.jp","Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. ohue@c.titech.ac.jp","Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8560, Japan. ohue@c.titech.ac.jp","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan. ohue@c.titech.ac.jp","institution_ids":["https://openalex.org/I4210112104"]},{"raw_affiliation_string":"Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. ohue@c.titech.ac.jp","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067025136","display_name":"Yutaka Akiyama","orcid":"https://orcid.org/0000-0003-2863-8703"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]},{"id":"https://openalex.org/I4210112104","display_name":"Innovative Research (United States)","ror":"https://ror.org/01zxe4w25","country_code":"US","type":"company","lineage":["https://openalex.org/I4210112104"]},{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP","US"],"is_corresponding":true,"raw_author_name":"Yutaka Akiyama","raw_affiliation_strings":["AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8560, Japan. akiyama@c.titech.ac.jp","Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan. akiyama@c.titech.ac.jp","Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. akiyama@c.titech.ac.jp","Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. akiyama@c.titech.ac.jp","Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. akiyama@c.titech.ac.jp","Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8560, Japan. akiyama@c.titech.ac.jp","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan. akiyama@c.titech.ac.jp","institution_ids":["https://openalex.org/I4210112104"]},{"raw_affiliation_string":"Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. akiyama@c.titech.ac.jp","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. akiyama@c.titech.ac.jp","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. akiyama@c.titech.ac.jp","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 W8-93 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5061510293","https://openalex.org/A5067025136"],"corresponding_institution_ids":["https://openalex.org/I114531698","https://openalex.org/I4210112104","https://openalex.org/I73613424"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.2359,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.78779554,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"19","issue":"S4","first_page":"62","last_page":"62"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6460000276565552,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6460000276565552,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.06279999762773514,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.05559999868273735,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.8201810121536255},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6816696524620056},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.6504898071289062},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5769708156585693},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5345659852027893},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.4917464554309845},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.46131277084350586},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.45401257276535034},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4330355226993561},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4255882203578949},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3937722146511078},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3351699709892273},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1834522783756256},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.15312302112579346},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0781097412109375}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.8201810121536255},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6816696524620056},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.6504898071289062},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5769708156585693},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5345659852027893},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.4917464554309845},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.46131277084350586},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.45401257276535034},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4330355226993561},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4255882203578949},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3937722146511078},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3351699709892273},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1834522783756256},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.15312302112579346},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0781097412109375},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-018-2073-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2073-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2073-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29745830","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29745830","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:7eda255d9da347c783d31a8a19ddba86","is_oa":true,"landing_page_url":"https://doaj.org/article/7eda255d9da347c783d31a8a19ddba86","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss S4, Pp 61-72 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4965297","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5998897","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5998897","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5998897","pdf_url":null,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2073-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2073-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2073-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2521286739","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320334789","funder_display_name":"Japan Science and Technology Agency"},{"id":"https://openalex.org/G2576085165","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G5081383656","display_name":"Development of computational methods for supporting druggable cyclic peptide design","funder_award_id":"17H01814","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6126637418","display_name":"Computational prediction of mitochondrial protein interactome","funder_award_id":"18K18149","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6718509927","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7879866177","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G8232900099","display_name":"Tropical diseases-related protein-protein interaction analysis by using exhaustive docking","funder_award_id":"16K00388","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G910305235","display_name":"Development of divide-and-conquer based docking method using common partial structures of hundreds of millions of compounds","funder_award_id":"17J06897","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320338244","display_name":"Research Complex Program","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2801631012.pdf","grobid_xml":"https://content.openalex.org/works/W2801631012.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W76842085","https://openalex.org/W1529184047","https://openalex.org/W1544046482","https://openalex.org/W1899503782","https://openalex.org/W1965379872","https://openalex.org/W1980308691","https://openalex.org/W1982267716","https://openalex.org/W1988469564","https://openalex.org/W1988739180","https://openalex.org/W1992424677","https://openalex.org/W2037036397","https://openalex.org/W2038555943","https://openalex.org/W2053884159","https://openalex.org/W2055654424","https://openalex.org/W2065279209","https://openalex.org/W2071097296","https://openalex.org/W2085419794","https://openalex.org/W2091710329","https://openalex.org/W2093730890","https://openalex.org/W2101181377","https://openalex.org/W2102791444","https://openalex.org/W2110336366","https://openalex.org/W2118545782","https://openalex.org/W2118839338","https://openalex.org/W2120973253","https://openalex.org/W2121753315","https://openalex.org/W2131989561","https://openalex.org/W2133712572","https://openalex.org/W2137885918","https://openalex.org/W2140883620","https://openalex.org/W2144119251","https://openalex.org/W2148356001","https://openalex.org/W2154139219","https://openalex.org/W2157122545","https://openalex.org/W2157253968","https://openalex.org/W2157991822","https://openalex.org/W2158714788","https://openalex.org/W2162392441","https://openalex.org/W2164255317","https://openalex.org/W2167869241","https://openalex.org/W2171778773","https://openalex.org/W2339738230","https://openalex.org/W2517814100","https://openalex.org/W2537623931","https://openalex.org/W2556480600","https://openalex.org/W2559588208","https://openalex.org/W2755729082","https://openalex.org/W2915536738"],"related_works":["https://openalex.org/W3181892255","https://openalex.org/W3132544722","https://openalex.org/W4389222350","https://openalex.org/W4388749535","https://openalex.org/W2103435205","https://openalex.org/W4375844720","https://openalex.org/W2013950502","https://openalex.org/W4389309199","https://openalex.org/W2084743099","https://openalex.org/W4285340733"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein-protein":[1],"interactions":[2],"(PPIs)":[3],"play":[4],"several":[5,119],"roles":[6],"in":[7,57,184],"living":[8],"cells,":[9],"and":[10,25,106,112,173,196,223,264,292,297,314,317],"computational":[11,91],"PPI":[12,34,64,74,92,155,168,178,186,225,236,283,300,304],"prediction":[13,75,104,187],"is":[14,66,95,210,318],"a":[15,99,132,271,278],"major":[16],"focus":[17],"of":[18,33,51,59,90,135,140,153,167,204,281,311],"many":[19],"researchers.":[20],"The":[21],"three-dimensional":[22],"(3D)":[23],"structure":[24,209],"binding":[26],"surface":[27],"are":[28,46,192],"important":[29],"for":[30,42,137,241,321],"the":[31,88,126,138,165,258,309],"design":[32],"inhibitors.":[35],"Therefore,":[36],"rigid":[37],"body":[38],"protein-protein":[39,79],"docking":[40,287],"calculations":[41,288],"two":[43],"protein":[44,194,208,244,260,315],"structures":[45,61,111,269],"expected":[47],"to":[48,85,97,102,113,176,295],"allow":[49],"elucidation":[50],"PPIs":[52,199,313],"different":[53],"from":[54,200],"known":[55,63,224,249],"complexes":[56],"terms":[58],"3D":[60,109,272],"because":[62],"information":[65],"not":[67,130],"explicitly":[68],"required.":[69],"We":[70],"have":[71],"developed":[72],"rapid":[73],"software":[76],"based":[77,285],"on":[78,261,286],"docking,":[80],"called":[81],"MEGADOCK.":[82],"In":[83,145,189],"order":[84],"fully":[86],"utilize":[87],"benefits":[89],"predictions,":[93,156,237],"it":[94],"necessary":[96],"construct":[98],"comprehensive":[100,282],"database":[101,152],"gather":[103],"results":[105],"their":[107],"predicted":[108,124,198,243,267],"complex":[110,268],"make":[114],"them":[115],"easily":[116,296],"accessible.":[117],"Although":[118],"databases":[120,128,172],"exist":[121],"that":[122,180,254],"provide":[123],"PPIs,":[125],"previous":[127,171],"do":[129],"contain":[131],"sufficient":[133],"number":[134,166],"entries":[136],"purpose":[139],"discovering":[141],"novel":[142],"PPIs.":[143],"RESULTS:":[144],"this":[146],"study,":[147],"we":[148],"constructed":[149],"an":[150,247],"integrated":[151],"MEGADOCK":[154],"named":[157],"MEGADOCK-Web.":[158],"MEGADOCK-Web":[159,228,276,306],"provides":[160,229,277],"more":[161],"than":[162,170],"10":[163],"times":[164],"predictions":[169,179,284],"enables":[174,293],"users":[175,294],"conduct":[177],"cannot":[181],"be":[182],"found":[183],"conventional":[185],"databases.":[188],"MEGADOCK-Web,":[190],"there":[191],"7528":[193],"chains":[195],"28,331,628":[197],"all":[201],"possible":[202],"combinations":[203],"those":[205],"proteins.":[206],"Each":[207],"annotated":[211],"with":[212,246,257,289],"PDB":[213],"ID,":[214,216],"chain":[215],"UniProt":[217],"AC,":[218],"related":[219],"KEGG":[220],"pathway":[221],"IDs,":[222],"pairs.":[226],"Additionally,":[227],"four":[230],"powerful":[231],"functions:":[232],"1)":[233],"searching":[234],"precalculated":[235],"2)":[238],"providing":[239],"annotations":[240],"each":[242],"pair":[245],"experimentally":[248],"PPI,":[250],"3)":[251],"visualizing":[252,266],"candidates":[253],"may":[255],"interact":[256],"query":[259],"biochemical":[262,290],"pathways,":[263],"4)":[265],"through":[270],"molecular":[273],"viewer.":[274],"CONCLUSION:":[275],"huge":[279],"amount":[280],"pathways":[291],"quickly":[298],"assess":[299],"feasibilities":[301],"by":[302],"archiving":[303],"predictions.":[305],"also":[307],"promotes":[308],"discovery":[310],"new":[312],"functions":[316],"freely":[319],"available":[320],"use":[322],"at":[323],"http://www.bi.cs.titech.ac.jp/megadock-web/":[324],".":[325]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
