{"id":"https://openalex.org/W2395425574","doi":"https://doi.org/10.1093/nar/gkw315","title":"The RING 2.0 web server for high quality residue interaction networks","display_name":"The RING 2.0 web server for high quality residue interaction networks","publication_year":2016,"publication_date":"2016-05-19","ids":{"openalex":"https://openalex.org/W2395425574","doi":"https://doi.org/10.1093/nar/gkw315","mag":"2395425574","pmid":"https://pubmed.ncbi.nlm.nih.gov/27198219"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkw315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw315","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W367/7632571/gkw315.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/44/W1/W367/7632571/gkw315.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000882827","display_name":"Damiano Piovesan","orcid":"https://orcid.org/0000-0001-8210-2390"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Damiano Piovesan","raw_affiliation_strings":["Department of Biomedical Sciences, University of Padua, Padua 35121, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, University of Padua, Padua 35121, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046118465","display_name":"Giovanni Minervini","orcid":"https://orcid.org/0000-0001-7013-5785"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giovanni Minervini","raw_affiliation_strings":["Department of Biomedical Sciences, University of Padua, Padua 35121, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, University of Padua, Padua 35121, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066560665","display_name":"Silvio C. E. Tosatto","orcid":"https://orcid.org/0000-0003-4525-7793"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]},{"id":"https://openalex.org/I4210113153","display_name":"Neuroscience Institute","ror":"https://ror.org/0240rwx68","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210113153","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Silvio\u00a0C.E. Tosatto","raw_affiliation_strings":["Department of Biomedical Sciences, University of Padua, Padua 35121, Italy CNR Institute of Neuroscience, Padua 35121, Italy silvio.tosatto@unipd.it","CNR Institute of Neuroscience, Padua 35121, Italy","Department of Biomedical Sciences, University of Padua, Padua 35121, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, University of Padua, Padua 35121, Italy CNR Institute of Neuroscience, Padua 35121, Italy silvio.tosatto@unipd.it","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"CNR Institute of Neuroscience, Padua 35121, Italy","institution_ids":["https://openalex.org/I4210113153"]},{"raw_affiliation_string":"Department of Biomedical Sciences, University of Padua, Padua 35121, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066560665"],"corresponding_institution_ids":["https://openalex.org/I138689650","https://openalex.org/I4210113153"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":22.1372,"has_fulltext":false,"cited_by_count":425,"citation_normalized_percentile":{"value":0.99623798,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"44","issue":"W1","first_page":"W367","last_page":"W374"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9987000226974487,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6802474856376648},{"id":"https://openalex.org/keywords/ring","display_name":"Ring (chemistry)","score":0.6632096171379089},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5283886790275574},{"id":"https://openalex.org/keywords/stacking","display_name":"Stacking","score":0.5227836966514587},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5016357898712158},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4514821469783783},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.39156976342201233},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34706369042396545},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2963063716888428},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1743394434452057},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14319974184036255},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09983795881271362}],"concepts":[{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6802474856376648},{"id":"https://openalex.org/C2780378348","wikidata":"https://www.wikidata.org/wiki/Q25351438","display_name":"Ring (chemistry)","level":2,"score":0.6632096171379089},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5283886790275574},{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.5227836966514587},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5016357898712158},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4514821469783783},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.39156976342201233},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34706369042396545},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2963063716888428},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1743394434452057},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14319974184036255},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09983795881271362},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":"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":"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":"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":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019925","descriptor_name":"Cyclin A","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019925","descriptor_name":"Cyclin A","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019925","descriptor_name":"Cyclin A","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019925","descriptor_name":"Cyclin A","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019925","descriptor_name":"Cyclin A","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019925","descriptor_name":"Cyclin A","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","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},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050760","descriptor_name":"Cyclin-Dependent Kinase Inhibitor p27","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050760","descriptor_name":"Cyclin-Dependent Kinase Inhibitor p27","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050760","descriptor_name":"Cyclin-Dependent Kinase Inhibitor p27","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050760","descriptor_name":"Cyclin-Dependent Kinase Inhibitor p27","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D050760","descriptor_name":"Cyclin-Dependent Kinase Inhibitor p27","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D050760","descriptor_name":"Cyclin-Dependent Kinase Inhibitor p27","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkw315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw315","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W367/7632571/gkw315.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:27198219","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27198219","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:3952875","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4987896","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:44/W1/W367","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/44/W1/W367","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:www.research.unipd.it:11577/3230655","is_oa":true,"landing_page_url":"http://hdl.handle.net/11577/3230655","pdf_url":null,"source":{"id":"https://openalex.org/S4377196283","display_name":"Research Padua  Archive (University of Padua)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"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":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkw315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw315","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W367/7632571/gkw315.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2395425574.pdf","grobid_xml":"https://content.openalex.org/works/W2395425574.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1536428180","https://openalex.org/W1966297170","https://openalex.org/W1982874561","https://openalex.org/W1983497040","https://openalex.org/W1984695931","https://openalex.org/W1987759430","https://openalex.org/W1996413533","https://openalex.org/W2000236879","https://openalex.org/W2001297798","https://openalex.org/W2008620264","https://openalex.org/W2008708467","https://openalex.org/W2021200484","https://openalex.org/W2030028095","https://openalex.org/W2038049686","https://openalex.org/W2043570667","https://openalex.org/W2045529907","https://openalex.org/W2049208809","https://openalex.org/W2049277949","https://openalex.org/W2065769502","https://openalex.org/W2077349723","https://openalex.org/W2085038958","https://openalex.org/W2099677428","https://openalex.org/W2109872885","https://openalex.org/W2110869427","https://openalex.org/W2111554317","https://openalex.org/W2115339329","https://openalex.org/W2119915462","https://openalex.org/W2128705810","https://openalex.org/W2129020329","https://openalex.org/W2130359029","https://openalex.org/W2143185848","https://openalex.org/W2145602919","https://openalex.org/W2146891463","https://openalex.org/W2148866967","https://openalex.org/W2151065895","https://openalex.org/W2158714788","https://openalex.org/W2159675211","https://openalex.org/W2162262059","https://openalex.org/W2166997231","https://openalex.org/W3103071483"],"related_works":["https://openalex.org/W2035329725","https://openalex.org/W4376641153","https://openalex.org/W2050788868","https://openalex.org/W4250391473","https://openalex.org/W4302292679","https://openalex.org/W2956222435","https://openalex.org/W4241625287","https://openalex.org/W2027634686","https://openalex.org/W2952283344","https://openalex.org/W2037378534"],"abstract_inverted_index":{"Residue":[0],"interaction":[1],"networks":[2,86],"(RINs)":[3],"are":[4,14,87,169],"an":[5,122,164],"alternative":[6],"way":[7],"of":[8,46,53,98],"representing":[9],"protein":[10,31,59],"structures":[11],"where":[12],"nodes":[13],"residues":[15],"and":[16,24,35,55,64,72,76,81,90,160,167],"arcs":[17],"physico-chemical":[18],"interactions.":[19,66],"RINs":[20],"have":[21],"been":[22],"extensively":[23],"successfully":[25],"used":[26],"for":[27,50,145],"analysing":[28],"mutation":[29],"effects,":[30],"folding,":[32],"domain-domain":[33],"communication":[34],"catalytic":[36],"activity.":[37],"Here":[38],"we":[39],"present":[40],"RING":[41,48,67,110],"2.0,":[42],"a":[43,94],"new":[44],"version":[45],"the":[47,51,103,118,127,136,142,149,155],"software":[49],"identification":[52],"covalent":[54],"non-covalent":[56],"bonds":[57],"in":[58,135,139,154],"structures,":[60],"including":[61,79],"\u03c0-\u03c0":[62],"stacking":[63],"\u03c0-cation":[65],"2.0":[68],"is":[69,112],"extremely":[70],"fast":[71],"generates":[73],"both":[74],"intra":[75],"inter-chain":[77],"interactions":[78,150],"solvent":[80],"ligand":[82],"atoms.":[83],"The":[84,129,157],"generated":[85,113],"very":[88],"accurate":[89],"reliable":[91],"thanks":[92],"to":[93,125],"complex":[95],"empirical":[96],"re-parameterization":[97],"distance":[99],"thresholds":[100],"performed":[101],"on":[102],"entire":[104],"Protein":[105],"Data":[106],"Bank.":[107],"By":[108],"default,":[109],"output":[111],"with":[114,163],"optimal":[115],"parameters":[116],"but":[117],"web":[119,158],"server":[120,159],"provides":[121],"exhaustive":[123],"interface":[124],"customize":[126],"calculation.":[128],"network":[130],"can":[131],"be":[132],"visualized":[133],"directly":[134],"browser":[137],"or":[138],"Cytoscape.":[140],"Alternatively,":[141],"RING-Viz":[143],"script":[144],"Pymol":[146],"allows":[147],"visualizing":[148],"at":[151],"atomic":[152],"level":[153],"structure.":[156],"RING-Viz,":[161],"together":[162],"extensive":[165],"help":[166],"tutorial,":[168],"available":[170],"from":[171],"URL:":[172],"http://protein.bio.unipd.it/ring.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":28},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":34},{"year":2022,"cited_by_count":65},{"year":2021,"cited_by_count":72},{"year":2020,"cited_by_count":66},{"year":2019,"cited_by_count":58},{"year":2018,"cited_by_count":43},{"year":2017,"cited_by_count":24}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}