{"id":"https://openalex.org/W3087201089","doi":"https://doi.org/10.1186/s12859-020-03600-8","title":"The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses","display_name":"The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses","publication_year":2020,"publication_date":"2020-09-01","ids":{"openalex":"https://openalex.org/W3087201089","doi":"https://doi.org/10.1186/s12859-020-03600-8","mag":"3087201089","pmid":"https://pubmed.ncbi.nlm.nih.gov/32938371"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03600-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03600-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03600-8","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/s12859-020-03600-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023132821","display_name":"Didier Barradas\u2010Bautista","orcid":"https://orcid.org/0000-0002-6464-6607"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Didier Barradas-Bautista","raw_affiliation_strings":["KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007213740","display_name":"Zhen Cao","orcid":"https://orcid.org/0000-0002-9341-3634"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Zhen Cao","raw_affiliation_strings":["KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053222658","display_name":"Luigi Cavallo","orcid":"https://orcid.org/0000-0002-1398-338X"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Luigi Cavallo","raw_affiliation_strings":["KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071471999","display_name":"Romina Oliva","orcid":"https://orcid.org/0000-0002-6156-6249"},"institutions":[{"id":"https://openalex.org/I183638586","display_name":"Parthenope University of Naples","ror":"https://ror.org/05pcv4v03","country_code":"IT","type":"education","lineage":["https://openalex.org/I183638586"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Romina Oliva","raw_affiliation_strings":["Department of Sciences and Technologies, University of Naples \"Parthenope\", Centro Direzionale - Isola C4, 80143, Naples, Italy. romina.oliva@uniparthenope.it","Department of Sciences and Technologies, University of Naples \"Parthenope\", Centro Direzionale - Isola C4, 80143, Naples, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Sciences and Technologies, University of Naples \"Parthenope\", Centro Direzionale - Isola C4, 80143, Naples, Italy. romina.oliva@uniparthenope.it","institution_ids":["https://openalex.org/I183638586"]},{"raw_affiliation_string":"Department of Sciences and Technologies, University of Naples \"Parthenope\", Centro Direzionale - Isola C4, 80143, Naples, Italy","institution_ids":["https://openalex.org/I183638586"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5071471999"],"corresponding_institution_ids":["https://openalex.org/I183638586"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.0116,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.82059635,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"21","issue":"S8","first_page":"262","last_page":"262"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9686999917030334,"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/pipeline","display_name":"Pipeline (software)","score":0.6410269737243652},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.6250311732292175},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6093255281448364},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5877307653427124},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4118475914001465},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38468119502067566},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2493617832660675},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.206022709608078},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.081179678440094}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6410269737243652},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.6250311732292175},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6093255281448364},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5877307653427124},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4118475914001465},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38468119502067566},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2493617832660675},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.206022709608078},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.081179678440094},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-020-03600-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03600-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03600-8","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:32938371","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32938371","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:a4be45632fa44c6f8950f3b75e3337c9","is_oa":true,"landing_page_url":"https://doaj.org/article/a4be45632fa44c6f8950f3b75e3337c9","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 21, Iss S8, Pp 1-18 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7493188","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7493188","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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"},{"id":"pmh:oai:repository.kaust.edu.sa:10754/665269","is_oa":true,"landing_page_url":"http://hdl.handle.net/10754/665269","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"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":"","raw_type":"Article"},{"id":"pmh:oai:ricerca.uniparthenope.it:11367/86253","is_oa":false,"landing_page_url":"http://hdl.handle.net/11367/86253","pdf_url":null,"source":{"id":"https://openalex.org/S4377196432","display_name":"CINECA IRIS Institutial research information system (Parthenope University of Naples)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I183638586","host_organization_name":"Parthenope University of Naples","host_organization_lineage":["https://openalex.org/I183638586"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03600-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03600-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03600-8","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/G3056429611","display_name":null,"funder_award_id":"FFABR","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G3935855236","display_name":null,"funder_award_id":"FFABR \u201cFondo per il Finanziamento Attivit\u00e0 Base di Ricerca\u201d","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G4744821971","display_name":null,"funder_award_id":"baseline","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3087201089.pdf","grobid_xml":"https://content.openalex.org/works/W3087201089.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1194601030","https://openalex.org/W1644470444","https://openalex.org/W1843273176","https://openalex.org/W2009405916","https://openalex.org/W2015934148","https://openalex.org/W2016385245","https://openalex.org/W2024911966","https://openalex.org/W2027045099","https://openalex.org/W2027403155","https://openalex.org/W2048643046","https://openalex.org/W2054118816","https://openalex.org/W2054394841","https://openalex.org/W2076710572","https://openalex.org/W2081320767","https://openalex.org/W2083734879","https://openalex.org/W2091634201","https://openalex.org/W2096134087","https://openalex.org/W2100025509","https://openalex.org/W2101288419","https://openalex.org/W2114027069","https://openalex.org/W2126081368","https://openalex.org/W2129562311","https://openalex.org/W2130479394","https://openalex.org/W2133312664","https://openalex.org/W2137004773","https://openalex.org/W2137167381","https://openalex.org/W2160868144","https://openalex.org/W2171268876","https://openalex.org/W2343238565","https://openalex.org/W2554109484","https://openalex.org/W2557083319","https://openalex.org/W2611400920","https://openalex.org/W2767509030","https://openalex.org/W2774178591","https://openalex.org/W2980678340","https://openalex.org/W3201413583","https://openalex.org/W4230638849"],"related_works":["https://openalex.org/W3037187668","https://openalex.org/W2804364458","https://openalex.org/W4298130764","https://openalex.org/W2132641928","https://openalex.org/W4310225030","https://openalex.org/W2090259340","https://openalex.org/W2083665254","https://openalex.org/W2393816671","https://openalex.org/W1534720161","https://openalex.org/W1926736923"],"abstract_inverted_index":{"Introducing":[0],"some":[1],"flexibility":[2],"in":[3],"the":[4,14,20,23,49],"final":[5],"model":[6],"selection":[7],"and":[8,51],"ranking,":[9],"as":[10,12,31],"well":[11],"differentiating":[13],"adopted":[15],"scoring":[16],"approach":[17,38],"depending":[18],"on":[19,44],"targets":[21],"were":[22],"key":[24],"assets":[25],"for":[26],"our":[27],"highly":[28],"successful":[29],"performance,":[30],"compared":[32],"to":[33,48],"previous":[34],"CAPRI":[35],"rounds.":[36],"The":[37],"we":[39],"propose":[40],"is":[41],"entirely":[42],"based":[43],"methods":[45],"made":[46],"available":[47],"community":[50],"could":[52],"thus":[53],"be":[54],"reproduced":[55],"by":[56],"any":[57],"user.":[58]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
