{"id":"https://openalex.org/W4387300238","doi":"https://doi.org/10.1093/bioinformatics/btad608","title":"Surfaces: a software to quantify and visualize interactions within and between proteins and ligands","display_name":"Surfaces: a software to quantify and visualize interactions within and between proteins and ligands","publication_year":2023,"publication_date":"2023-09-29","ids":{"openalex":"https://openalex.org/W4387300238","doi":"https://doi.org/10.1093/bioinformatics/btad608","pmid":"https://pubmed.ncbi.nlm.nih.gov/37788107"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad608","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad608","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad608/51839182/btad608.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/btad608/51839182/btad608.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036098132","display_name":"Nat\u00e1lia Teruel","orcid":"https://orcid.org/0000-0003-3485-973X"},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Nat\u00e1lia Teruel","raw_affiliation_strings":["Department of Pharmacology and Physiology, Faculty of Medicine, Universit\u00e9 de Montr\u00e9al , Montreal H3T 1J4,","Department of Pharmacology and Physiology, Faculty of Medicine, Universit\u00e9 de Montr\u00e9al , Montreal H3T 1J4, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Physiology, Faculty of Medicine, Universit\u00e9 de Montr\u00e9al , Montreal H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Department of Pharmacology and Physiology, Faculty of Medicine, Universit\u00e9 de Montr\u00e9al , Montreal H3T 1J4, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101661383","display_name":"Vin\u00edcius Magalh\u00e3es Borges","orcid":"https://orcid.org/0000-0002-9502-2549"},"institutions":[{"id":"https://openalex.org/I88694374","display_name":"Marshall University","ror":"https://ror.org/02erqft81","country_code":"US","type":"education","lineage":["https://openalex.org/I88694374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vinicius Magalh\u00e3es Borges","raw_affiliation_strings":["Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University , Huntington, WV,","Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University , Huntington, WV, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University , Huntington, WV,","institution_ids":["https://openalex.org/I88694374"]},{"raw_affiliation_string":"Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University , Huntington, WV, USA","institution_ids":["https://openalex.org/I88694374"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019812910","display_name":"Rafa\u00ebl Najmanovich","orcid":"https://orcid.org/0000-0002-6971-7224"},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Rafael Najmanovich","raw_affiliation_strings":["Department of Pharmacology and Physiology, Faculty of Medicine, Universit\u00e9 de Montr\u00e9al , Montreal H3T 1J4,","Department of Pharmacology and Physiology, Faculty of Medicine, Universit\u00e9 de Montr\u00e9al , Montreal H3T 1J4, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Physiology, Faculty of Medicine, Universit\u00e9 de Montr\u00e9al , Montreal H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Department of Pharmacology and Physiology, Faculty of Medicine, Universit\u00e9 de Montr\u00e9al , Montreal H3T 1J4, Canada","institution_ids":["https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5036098132"],"corresponding_institution_ids":["https://openalex.org/I70931966"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.1199,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.94349509,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13127","display_name":"Biotin and Related Studies","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T13127","display_name":"Biotin and Related Studies","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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":0.9923999905586243,"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":0.9782999753952026,"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/visualization","display_name":"Visualization","score":0.7940632104873657},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7535532712936401},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.6938920021057129},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6563408374786377},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6418832540512085},{"id":"https://openalex.org/keywords/software-visualization","display_name":"Software visualization","score":0.47518980503082275},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4148203730583191},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.41260966658592224},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.32909393310546875},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3138960599899292},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.30074217915534973},{"id":"https://openalex.org/keywords/software-development","display_name":"Software development","score":0.19518578052520752},{"id":"https://openalex.org/keywords/component-based-software-engineering","display_name":"Component-based software engineering","score":0.10232892632484436},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07624104619026184}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7940632104873657},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7535532712936401},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.6938920021057129},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6563408374786377},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6418832540512085},{"id":"https://openalex.org/C4379982","wikidata":"https://www.wikidata.org/wiki/Q1273511","display_name":"Software visualization","level":5,"score":0.47518980503082275},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4148203730583191},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.41260966658592224},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.32909393310546875},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3138960599899292},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.30074217915534973},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.19518578052520752},{"id":"https://openalex.org/C174683762","wikidata":"https://www.wikidata.org/wiki/Q609588","display_name":"Component-based software engineering","level":4,"score":0.10232892632484436},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07624104619026184},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":"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":"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":"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":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":"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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad608","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad608","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad608/51839182/btad608.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:37788107","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37788107","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:pubmedcentral.nih.gov:10568369","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10568369","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10568369/pdf/btad608.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/btad608","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad608","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad608/51839182/btad608.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":[],"awards":[{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G8284766523","display_name":null,"funder_award_id":"(NSERC)","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320314000","display_name":"Compute Canada","ror":"https://ror.org/03ty8yr27"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4387300238.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1507991774","https://openalex.org/W1969046853","https://openalex.org/W1975580333","https://openalex.org/W1993046136","https://openalex.org/W1994891218","https://openalex.org/W2008505479","https://openalex.org/W2023490488","https://openalex.org/W2038542598","https://openalex.org/W2042335204","https://openalex.org/W2070348176","https://openalex.org/W2077058244","https://openalex.org/W2095719702","https://openalex.org/W2099471962","https://openalex.org/W2103183317","https://openalex.org/W2125677968","https://openalex.org/W2134059200","https://openalex.org/W2151550848","https://openalex.org/W2164507558","https://openalex.org/W2168374535","https://openalex.org/W2201713963","https://openalex.org/W2283896596","https://openalex.org/W2558963911","https://openalex.org/W2788217325","https://openalex.org/W2803284534","https://openalex.org/W2914298720","https://openalex.org/W2949226104","https://openalex.org/W2979865805","https://openalex.org/W3082869193","https://openalex.org/W3137338205","https://openalex.org/W3164567672","https://openalex.org/W3169539391","https://openalex.org/W3201270194","https://openalex.org/W4205926854","https://openalex.org/W4206542177","https://openalex.org/W4212975596","https://openalex.org/W4283828269","https://openalex.org/W4286382909","https://openalex.org/W4381620636","https://openalex.org/W4384405818","https://openalex.org/W4392283093","https://openalex.org/W6782748463"],"related_works":["https://openalex.org/W2386674074","https://openalex.org/W834755178","https://openalex.org/W2064191515","https://openalex.org/W1984601109","https://openalex.org/W2033226981","https://openalex.org/W1867947061","https://openalex.org/W2004099228","https://openalex.org/W4286008520","https://openalex.org/W4312541014","https://openalex.org/W4285288679"],"abstract_inverted_index":{"All":[0],"scripts":[1],"are":[2],"available":[3,9],"at":[4,10],"https://github.com/NRGLab/Surfaces.":[5],"Surface's":[6],"documentation":[7],"is":[8],"https://surfaces-tutorial.readthedocs.io/en/latest/index.html.":[11]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
