{"id":"https://openalex.org/W2565027487","doi":"https://doi.org/10.1093/bioinformatics/btw756","title":"The PPI3D web server for searching, analyzing and modeling protein\u2013protein interactions in the context of 3D structures","display_name":"The PPI3D web server for searching, analyzing and modeling protein\u2013protein interactions in the context of 3D structures","publication_year":2016,"publication_date":"2016-11-22","ids":{"openalex":"https://openalex.org/W2565027487","doi":"https://doi.org/10.1093/bioinformatics/btw756","mag":"2565027487","pmid":"https://pubmed.ncbi.nlm.nih.gov/28011769"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw756","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw756","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/6/935/25147921/btw756.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/6/935/25147921/btw756.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091513476","display_name":"Justas Dapk\u016bnas","orcid":"https://orcid.org/0000-0002-0496-6107"},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Justas Dapk\u016bnas","raw_affiliation_strings":["Institute of Biotechnology, Vilnius University, Vilnius, Lithuania"],"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Vilnius University, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022379440","display_name":"Albertas Timinskas","orcid":null},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Albertas Timinskas","raw_affiliation_strings":["Institute of Biotechnology, Vilnius University, Vilnius, Lithuania"],"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Vilnius University, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079599346","display_name":"Kliment Olechnovi\u010d","orcid":"https://orcid.org/0000-0003-4918-9505"},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Kliment Olechnovi\u010d","raw_affiliation_strings":["Faculty of Mathematics and Informatics, Vilnius University, Vilnius, Lithuania","Institute of Biotechnology, Vilnius University, Vilnius, Lithuania"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Informatics, Vilnius University, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]},{"raw_affiliation_string":"Institute of Biotechnology, Vilnius University, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055704497","display_name":"Mindaugas Margelevi\u010dius","orcid":"https://orcid.org/0000-0003-4981-6708"},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Mindaugas Margelevi\u010dius","raw_affiliation_strings":["Institute of Biotechnology, Vilnius University, Vilnius, Lithuania"],"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Vilnius University, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090395952","display_name":"Rytis Di\u010di\u016bnas","orcid":null},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Rytis Di\u010di\u016bnas","raw_affiliation_strings":["Institute of Biotechnology, Vilnius University, Vilnius, Lithuania"],"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Vilnius University, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031938940","display_name":"\u010ceslovas Venclovas","orcid":"https://orcid.org/0000-0002-4215-0213"},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":true,"raw_author_name":"\u010ceslovas Venclovas","raw_affiliation_strings":["Institute of Biotechnology, Vilnius University, Vilnius, Lithuania"],"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Vilnius University, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5031938940"],"corresponding_institution_ids":["https://openalex.org/I173212132"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.6673,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.84773262,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"33","issue":"6","first_page":"935","last_page":"937"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9984999895095825,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9984999895095825,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9979000091552734,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9948999881744385,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7835719585418701},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6112707257270813},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5793150663375854},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5694970488548279},{"id":"https://openalex.org/keywords/voronoi-diagram","display_name":"Voronoi diagram","score":0.5350103974342346},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.5258342027664185},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5096869468688965},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47865617275238037},{"id":"https://openalex.org/keywords/data-redundancy","display_name":"Data redundancy","score":0.46848878264427185},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3616560101509094},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2899323105812073},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2713363766670227},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18109017610549927},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1218145489692688},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11866167187690735}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7835719585418701},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6112707257270813},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5793150663375854},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5694970488548279},{"id":"https://openalex.org/C24881265","wikidata":"https://www.wikidata.org/wiki/Q757267","display_name":"Voronoi diagram","level":2,"score":0.5350103974342346},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.5258342027664185},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5096869468688965},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47865617275238037},{"id":"https://openalex.org/C7545210","wikidata":"https://www.wikidata.org/wiki/Q838123","display_name":"Data redundancy","level":2,"score":0.46848878264427185},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3616560101509094},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2899323105812073},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2713363766670227},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18109017610549927},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1218145489692688},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11866167187690735},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"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":"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":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw756","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw756","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/6/935/25147921/btw756.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28011769","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28011769","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw756","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw756","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/6/935/25147921/btw756.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2565027487.pdf","grobid_xml":"https://content.openalex.org/works/W2565027487.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1829437510","https://openalex.org/W2015714288","https://openalex.org/W2039063819","https://openalex.org/W2046301150","https://openalex.org/W2081290596","https://openalex.org/W2093916754","https://openalex.org/W2113267464","https://openalex.org/W2142678478","https://openalex.org/W2144046885","https://openalex.org/W2144954642","https://openalex.org/W2156125289","https://openalex.org/W2161072217","https://openalex.org/W2164939816","https://openalex.org/W2513068186"],"related_works":["https://openalex.org/W2002428578","https://openalex.org/W2897258045","https://openalex.org/W2018406690","https://openalex.org/W2072332896","https://openalex.org/W2951748633","https://openalex.org/W2542042335","https://openalex.org/W4292309272","https://openalex.org/W2057691131","https://openalex.org/W2952039693","https://openalex.org/W4280621979"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
