{"id":"https://openalex.org/W2776971422","doi":"https://doi.org/10.1515/bams-2017-0022","title":"Mechanism of ligand binding \u2013 PDZ domain taken as example","display_name":"Mechanism of ligand binding \u2013 PDZ domain taken as example","publication_year":2017,"publication_date":"2017-12-01","ids":{"openalex":"https://openalex.org/W2776971422","doi":"https://doi.org/10.1515/bams-2017-0022","mag":"2776971422"},"language":"en","primary_location":{"id":"doi:10.1515/bams-2017-0022","is_oa":false,"landing_page_url":"https://doi.org/10.1515/bams-2017-0022","pdf_url":null,"source":{"id":"https://openalex.org/S2764861201","display_name":"Bio-Algorithms and Med-Systems","issn_l":"1895-9091","issn":["1895-9091","1896-530X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bio-Algorithms and Med-Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://ruj.uj.edu.pl/xmlui/handle/item/142439","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071526721","display_name":"Dawid Du\u0142ak","orcid":null},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Dawid Du\u0142ak","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068559370","display_name":"Mateusz Banach","orcid":"https://orcid.org/0000-0003-1806-9877"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Mateusz Banach","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062765045","display_name":"Zdzis\u0142aw Wi\u015bniowski","orcid":"https://orcid.org/0000-0002-7278-6888"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Zdzis\u0142aw Wi\u015bniowski","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027144155","display_name":"Leszek Konieczny","orcid":null},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Leszek Konieczny","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087239926","display_name":"Irena Roterman","orcid":"https://orcid.org/0000-0003-3652-9099"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Irena Roterman","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland","institution_ids":["https://openalex.org/I126596746"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5087239926"],"corresponding_institution_ids":["https://openalex.org/I126596746"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1490896,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"13","issue":"4","first_page":"175","last_page":"178"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9782999753952026,"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":0.9782999753952026,"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/T10423","display_name":"Neurobiology and Insect Physiology Research","score":0.9241999983787537,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9092000126838684,"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/pentapeptide-repeat","display_name":"Pentapeptide repeat","score":0.8613690137863159},{"id":"https://openalex.org/keywords/pdz-domain","display_name":"PDZ domain","score":0.8504678010940552},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5875394344329834},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5261306762695312},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.48103979229927063},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.4428889751434326},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.369029700756073},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.35054710507392883},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.26940464973449707},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.23959773778915405},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2356339395046234},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.11557120084762573},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08292314410209656},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07789203524589539}],"concepts":[{"id":"https://openalex.org/C45197812","wikidata":"https://www.wikidata.org/wiki/Q24787539","display_name":"Pentapeptide repeat","level":3,"score":0.8613690137863159},{"id":"https://openalex.org/C154428179","wikidata":"https://www.wikidata.org/wiki/Q24721050","display_name":"PDZ domain","level":2,"score":0.8504678010940552},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5875394344329834},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5261306762695312},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.48103979229927063},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.4428889751434326},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.369029700756073},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.35054710507392883},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.26940464973449707},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.23959773778915405},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2356339395046234},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.11557120084762573},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08292314410209656},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07789203524589539},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1515/bams-2017-0022","is_oa":false,"landing_page_url":"https://doi.org/10.1515/bams-2017-0022","pdf_url":null,"source":{"id":"https://openalex.org/S2764861201","display_name":"Bio-Algorithms and Med-Systems","issn_l":"1895-9091","issn":["1895-9091","1896-530X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bio-Algorithms and Med-Systems","raw_type":"journal-article"},{"id":"pmh:oai:ruj.uj.edu.pl:item/142439","is_oa":true,"landing_page_url":"https://ruj.uj.edu.pl/xmlui/handle/item/142439","pdf_url":null,"source":{"id":"https://openalex.org/S4306401249","display_name":"Jagiellonian University Repository (Jagiellonian University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126596746","host_organization_name":"Jagiellonian University","host_organization_lineage":["https://openalex.org/I126596746"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:ruj.uj.edu.pl:item/126300","is_oa":true,"landing_page_url":"https://ruj.uj.edu.pl/xmlui/handle/item/126300","pdf_url":null,"source":{"id":"https://openalex.org/S4306401249","display_name":"Jagiellonian University Repository (Jagiellonian University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126596746","host_organization_name":"Jagiellonian University","host_organization_lineage":["https://openalex.org/I126596746"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:ruj.uj.edu.pl:item/96710","is_oa":false,"landing_page_url":"https://ruj.uj.edu.pl/xmlui/handle/item/96710","pdf_url":null,"source":{"id":"https://openalex.org/S4306400316","display_name":"Homo Politicus (Academy of Humanities and Economics in Lodz)","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":"artyku\u0142 w czasopi\u015bmie"}],"best_oa_location":{"id":"pmh:oai:ruj.uj.edu.pl:item/142439","is_oa":true,"landing_page_url":"https://ruj.uj.edu.pl/xmlui/handle/item/142439","pdf_url":null,"source":{"id":"https://openalex.org/S4306401249","display_name":"Jagiellonian University Repository (Jagiellonian University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126596746","host_organization_name":"Jagiellonian University","host_organization_lineage":["https://openalex.org/I126596746"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation","score":0.5299999713897705}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W175377976","https://openalex.org/W1965555277","https://openalex.org/W2034967903","https://openalex.org/W2038147869","https://openalex.org/W2061762615","https://openalex.org/W2065989745","https://openalex.org/W2110114468","https://openalex.org/W2154063883","https://openalex.org/W2156954132","https://openalex.org/W2159076012","https://openalex.org/W2242664669","https://openalex.org/W2282801158","https://openalex.org/W2533198818","https://openalex.org/W2765673662","https://openalex.org/W2944782266","https://openalex.org/W4240128943"],"related_works":["https://openalex.org/W2913537206","https://openalex.org/W2014235532","https://openalex.org/W1981740764","https://openalex.org/W2275510245","https://openalex.org/W2207139036","https://openalex.org/W2162151490","https://openalex.org/W2066353226","https://openalex.org/W2115050780","https://openalex.org/W2132186283","https://openalex.org/W2064058502"],"abstract_inverted_index":{"Abstract":[0],"The":[1,28,54],"mechanism":[2],"of":[3,69],"specific":[4],"ligand":[5],"binding":[6],"by":[7,36,47,51],"proteins":[8],"is":[9,20,39,56],"discussed":[10],"using":[11],"the":[12,16,24,33,59,66],"PDZ":[13],"domain":[14],"complexing":[15],"pentapeptide.":[17,53],"This":[18],"process":[19],"critical":[21],"for":[22],"clustering":[23],"membrane":[25],"ion":[26],"channel.":[27],"traditional":[29],"model":[30,63],"based":[31,57],"on":[32,58],"Beta-sheet":[34],"extension":[35,45],"complexed":[37,52],"pentapeptide":[38],"interpreted":[40],"as":[41],"a":[42],"hydrophobic":[43],"core":[44],"supported":[46],"additional":[48],"Beta-strand":[49],"generated":[50],"explanation":[55],"fuzzy":[60],"oil":[61],"drop":[62],"applied":[64],"to":[65],"crystal":[67],"structure":[68],"PDZ-pentapeptide.":[70]},"counts_by_year":[],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}
