{"id":"https://openalex.org/W4388539886","doi":"https://doi.org/10.1093/bioinformatics/btad675","title":"PyPCN: protein contact networks in PyMOL","display_name":"PyPCN: protein contact networks in PyMOL","publication_year":2023,"publication_date":"2023-11-01","ids":{"openalex":"https://openalex.org/W4388539886","doi":"https://doi.org/10.1093/bioinformatics/btad675","pmid":"https://pubmed.ncbi.nlm.nih.gov/37941462"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad675","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad675","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad675/52952551/btad675.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad675/52952551/btad675.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000688174","display_name":"Serena Rosignoli","orcid":"https://orcid.org/0000-0002-0164-8998"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Serena Rosignoli","raw_affiliation_strings":["Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , 00185 Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , 00185 Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024682464","display_name":"Luisa Di Paola","orcid":"https://orcid.org/0000-0001-5329-8689"},"institutions":[{"id":"https://openalex.org/I155125353","display_name":"Universit\u00e0 Campus Bio-Medico","ror":"https://ror.org/04gqx4x78","country_code":"IT","type":"education","lineage":["https://openalex.org/I155125353"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luisa di Paola","raw_affiliation_strings":["Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, Universit\u00e0 Campus Bio-Medico di Roma , 00128 Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, Universit\u00e0 Campus Bio-Medico di Roma , 00128 Rome, Italy","institution_ids":["https://openalex.org/I155125353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067090345","display_name":"Alessandro Paiardini","orcid":"https://orcid.org/0000-0001-9078-7545"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessandro Paiardini","raw_affiliation_strings":["Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , 00185 Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, Sapienza University of Rome , 00185 Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000688174"],"corresponding_institution_ids":["https://openalex.org/I861853513"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9473,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.76426173,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"39","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9976999759674072,"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":0.9976999759674072,"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":0.9965000152587891,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9927999973297119,"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":0.7735409736633301},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.7504532933235168},{"id":"https://openalex.org/keywords/adjacency-matrix","display_name":"Adjacency matrix","score":0.6820571422576904},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.6070290803909302},{"id":"https://openalex.org/keywords/adjacency-list","display_name":"Adjacency list","score":0.5963649749755859},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5897915363311768},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5149677395820618},{"id":"https://openalex.org/keywords/graph-drawing","display_name":"Graph drawing","score":0.5005772113800049},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.46687835454940796},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics","score":0.44534486532211304},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4381335973739624},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.33608290553092957},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3080119490623474},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2079004943370819},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.18897122144699097}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7735409736633301},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.7504532933235168},{"id":"https://openalex.org/C180356752","wikidata":"https://www.wikidata.org/wiki/Q727035","display_name":"Adjacency matrix","level":3,"score":0.6820571422576904},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.6070290803909302},{"id":"https://openalex.org/C110484373","wikidata":"https://www.wikidata.org/wiki/Q264398","display_name":"Adjacency list","level":2,"score":0.5963649749755859},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5897915363311768},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5149677395820618},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.5005772113800049},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.46687835454940796},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.44534486532211304},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4381335973739624},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.33608290553092957},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3080119490623474},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2079004943370819},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.18897122144699097}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad675","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad675","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad675/52952551/btad675.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37941462","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37941462","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},{"id":"pmh:oai:iris.uniroma1.it:11573/1691811","is_oa":true,"landing_page_url":"https://hdl.handle.net/11573/1691811","pdf_url":"https://iris.uniroma1.it/bitstream/11573/1691811/2/Rosignoli_PyPCN_2023.pdf","source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10641099","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10641099","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10641099/pdf/btad675.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad675","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad675","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad675/52952551/btad675.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6100000143051147,"display_name":"Life below water","id":"https://metadata.un.org/sdg/14"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4388539886.pdf"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W583735126","https://openalex.org/W1984695931","https://openalex.org/W1987254833","https://openalex.org/W1991605720","https://openalex.org/W2043046112","https://openalex.org/W2043570667","https://openalex.org/W2101414808","https://openalex.org/W2105012577","https://openalex.org/W2120580263","https://openalex.org/W2130479394","https://openalex.org/W2325652290","https://openalex.org/W2345718491","https://openalex.org/W2417513559","https://openalex.org/W2581672095","https://openalex.org/W2811167683","https://openalex.org/W3028330589","https://openalex.org/W3119119048","https://openalex.org/W3128563282","https://openalex.org/W3175059609","https://openalex.org/W3177828909","https://openalex.org/W4226027101","https://openalex.org/W4284899542","https://openalex.org/W4286217199","https://openalex.org/W4309908854","https://openalex.org/W4321225265"],"related_works":["https://openalex.org/W4213150077","https://openalex.org/W2369410163","https://openalex.org/W2982430984","https://openalex.org/W2078477160","https://openalex.org/W2059018062","https://openalex.org/W2604585036","https://openalex.org/W1991172810","https://openalex.org/W125803343","https://openalex.org/W1989103179","https://openalex.org/W2117632582"],"abstract_inverted_index":{"https://github.com/pcnproject/PyPCN.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}
