{"id":"https://openalex.org/W2059911899","doi":"https://doi.org/10.1021/ci200444d","title":"SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs","display_name":"SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs","publication_year":2012,"publication_date":"2012-02-01","ids":{"openalex":"https://openalex.org/W2059911899","doi":"https://doi.org/10.1021/ci200444d","mag":"2059911899","pmid":"https://pubmed.ncbi.nlm.nih.gov/22296449"},"language":"en","primary_location":{"id":"doi:10.1021/ci200444d","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200444d","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://lirias.kuleuven.be/handle/123456789/418105","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058986691","display_name":"David Sehnal","orcid":"https://orcid.org/0000-0002-0682-3089"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"David Sehnal","raw_affiliation_strings":["National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic"],"affiliations":[{"raw_affiliation_string":"National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051424845","display_name":"Radka Svobodov\u00e1 Va\u0159ekov\u00e1","orcid":"https://orcid.org/0000-0002-3840-8760"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]},{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Radka Svobodov\u00e1 Va\u0159ekov\u00e1","raw_affiliation_strings":["National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic"],"affiliations":[{"raw_affiliation_string":"National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045348857","display_name":"Heinrich J. Huber","orcid":"https://orcid.org/0000-0003-4454-2971"},"institutions":[{"id":"https://openalex.org/I142762351","display_name":"Royal College of Surgeons in Ireland","ror":"https://ror.org/01hxy9878","country_code":"IE","type":"education","lineage":["https://openalex.org/I142762351"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Heinrich J. Huber","raw_affiliation_strings":["Centre of Systems Medicine, Department of Physiology and Medical Physics, Royal\rCollege of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland","Centre of Systems Medicine, Department of Physiology and Medical Physics, Royal#R#College of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland"],"affiliations":[{"raw_affiliation_string":"Centre of Systems Medicine, Department of Physiology and Medical Physics, Royal\rCollege of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland","institution_ids":["https://openalex.org/I142762351"]},{"raw_affiliation_string":"Centre of Systems Medicine, Department of Physiology and Medical Physics, Royal#R#College of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland","institution_ids":["https://openalex.org/I142762351"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031789769","display_name":"Stanislav Geidl","orcid":null},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Stanislav Geidl","raw_affiliation_strings":["National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic"],"affiliations":[{"raw_affiliation_string":"National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077740452","display_name":"Crina-Maria Ionescu","orcid":null},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Crina-Maria Ionescu","raw_affiliation_strings":["National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic"],"affiliations":[{"raw_affiliation_string":"National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063010004","display_name":"Michaela Wimmerov\u00e1","orcid":"https://orcid.org/0000-0002-7108-4198"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Michaela Wimmerov\u00e1","raw_affiliation_strings":["National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic"],"affiliations":[{"raw_affiliation_string":"National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061853775","display_name":"Jaroslav Ko\u010da","orcid":"https://orcid.org/0000-0002-2780-4901"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Jaroslav Ko\u010da","raw_affiliation_strings":["National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic"],"affiliations":[{"raw_affiliation_string":"National Centre for Biomolecular\rResearch, Faculty of Science and CEITEC - Central European Institute\rof Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,\rCzech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"National Centre for Biomolecular#R#Research, Faculty of Science and CEITEC - Central European Institute#R#of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice,#R#Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5058986691"],"corresponding_institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"],"apc_list":null,"apc_paid":null,"fwci":0.8067,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.71335421,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"52","issue":"2","first_page":"343","last_page":"359"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9991999864578247,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9991999864578247,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9991000294685364,"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":0.9987999796867371,"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/computer-science","display_name":"Computer science","score":0.5803262591362},{"id":"https://openalex.org/keywords/superimposition","display_name":"Superimposition","score":0.5667600631713867},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.48970893025398254},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47874850034713745},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.47060948610305786},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46270230412483215},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.45937666296958923},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.45226824283599854},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.417169451713562},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3448055386543274},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3368212580680847},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27629464864730835},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2521904706954956},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24236303567886353},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1481836438179016},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13193416595458984}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5803262591362},{"id":"https://openalex.org/C143874112","wikidata":"https://www.wikidata.org/wiki/Q7643452","display_name":"Superimposition","level":2,"score":0.5667600631713867},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.48970893025398254},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47874850034713745},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.47060948610305786},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46270230412483215},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.45937666296958923},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.45226824283599854},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.417169451713562},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3448055386543274},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3368212580680847},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27629464864730835},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2521904706954956},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24236303567886353},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1481836438179016},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13193416595458984},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/ci200444d","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200444d","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:22296449","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22296449","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:epubs.rcsi.ie:physiolart-1019","is_oa":false,"landing_page_url":"https://epubs.rcsi.ie/cgi/viewcontent.cgi?article=1019&context=physiolart","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Physiology and Medical Physics Articles","raw_type":"text"},{"id":"pmh:oai:lirias2repo.kuleuven.be:123456789/418105","is_oa":true,"landing_page_url":"https://lirias.kuleuven.be/handle/123456789/418105","pdf_url":null,"source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"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":"Journal of Chemical Information and Modeling, vol. 52 (2), (343-359)","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"pmh:oai:lirias2repo.kuleuven.be:123456789/418105","is_oa":true,"landing_page_url":"https://lirias.kuleuven.be/handle/123456789/418105","pdf_url":null,"source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"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":"Journal of Chemical Information and Modeling, vol. 52 (2), (343-359)","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W1493926273","https://openalex.org/W1530397352","https://openalex.org/W1558853803","https://openalex.org/W1575639801","https://openalex.org/W1584236946","https://openalex.org/W1963538288","https://openalex.org/W1966078827","https://openalex.org/W1966521833","https://openalex.org/W1966680504","https://openalex.org/W1966790266","https://openalex.org/W1969404979","https://openalex.org/W1970492290","https://openalex.org/W1970654380","https://openalex.org/W1970829756","https://openalex.org/W1971458166","https://openalex.org/W1978462051","https://openalex.org/W1979147581","https://openalex.org/W1979734180","https://openalex.org/W1981967708","https://openalex.org/W1982603939","https://openalex.org/W1992907644","https://openalex.org/W1993267444","https://openalex.org/W2011952909","https://openalex.org/W2019342450","https://openalex.org/W2019345165","https://openalex.org/W2019616754","https://openalex.org/W2021954541","https://openalex.org/W2029087609","https://openalex.org/W2029667189","https://openalex.org/W2031595029","https://openalex.org/W2031901496","https://openalex.org/W2036411709","https://openalex.org/W2040644205","https://openalex.org/W2043199972","https://openalex.org/W2044098591","https://openalex.org/W2050330741","https://openalex.org/W2056807348","https://openalex.org/W2057568023","https://openalex.org/W2062359859","https://openalex.org/W2068049431","https://openalex.org/W2074231493","https://openalex.org/W2077743314","https://openalex.org/W2077754831","https://openalex.org/W2084598167","https://openalex.org/W2084651007","https://openalex.org/W2089198803","https://openalex.org/W2096039340","https://openalex.org/W2096725584","https://openalex.org/W2097108043","https://openalex.org/W2101449937","https://openalex.org/W2102333330","https://openalex.org/W2102597691","https://openalex.org/W2103626206","https://openalex.org/W2110397834","https://openalex.org/W2112084742","https://openalex.org/W2117319571","https://openalex.org/W2123121534","https://openalex.org/W2125696348","https://openalex.org/W2127067710","https://openalex.org/W2127597332","https://openalex.org/W2128175348","https://openalex.org/W2132256310","https://openalex.org/W2132629607","https://openalex.org/W2133035849","https://openalex.org/W2134155634","https://openalex.org/W2134623365","https://openalex.org/W2136567909","https://openalex.org/W2140407975","https://openalex.org/W2145955296","https://openalex.org/W2152326664","https://openalex.org/W2153245720","https://openalex.org/W2153251136","https://openalex.org/W2156611638","https://openalex.org/W2159506251","https://openalex.org/W2161370818","https://openalex.org/W2168514491","https://openalex.org/W2168802749","https://openalex.org/W2169545551","https://openalex.org/W2169762689","https://openalex.org/W2171004217","https://openalex.org/W2171985093","https://openalex.org/W2175644660","https://openalex.org/W2911312973","https://openalex.org/W4251903194"],"related_works":["https://openalex.org/W1065848034","https://openalex.org/W4238897586","https://openalex.org/W3105418574","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2105308189","https://openalex.org/W2148757883","https://openalex.org/W3085619796","https://openalex.org/W2091861424","https://openalex.org/W4235583582"],"abstract_inverted_index":{"There":[0],"is":[1,86,113,132,258,279],"a":[2,35,53,144,228,280],"paramount":[3],"need":[4],"to":[5,134,137,273],"develop":[6],"new":[7],"techniques":[8],"and":[9,105,148,153,164,169,214,224,245,292],"tools":[10],"that":[11,60,98,217,247,277],"will":[12,102],"extract":[13],"as":[14,17],"much":[15],"information":[16],"possible":[18],"from":[19,267],"the":[20,32,39,57,62,68,99,127,161,173,191,202,218,248,252,255,275,284],"ever":[21],"growing":[22],"repository":[23],"of":[24,34,42,45,83,139,166,176,183,193,204,222,254,287],"protein":[25,46,140],"3D":[26],"structures.":[27],"We":[28,121,188,199,236],"report":[29],"here":[30],"on":[31],"development":[33],"software":[36],"tool":[37],"for":[38,56,71,93,181,283],"multiple":[40],"superimposition":[41,50,175],"large":[43],"sets":[44],"structural":[47,141,281],"motifs.":[48,187],"Our":[49,156,270],"methodology":[51,125,168],"performs":[52],"systematic":[54],"search":[55],"atom":[58,257],"pairing":[59],"provides":[61,150],"best":[63,100],"fit.":[64],"During":[65],"this":[66,124],"search,":[67],"RMSD":[69],"values":[70],"all":[72],"chemically":[73],"relevant":[74],"pairings":[75,85],"are":[76],"calculated":[77],"by":[78,89,172],"quaternion":[79],"algebra.":[80],"The":[81],"number":[82],"evaluated":[84],"markedly":[87],"decreased":[88],"using":[90,195],"PDB":[91],"annotations":[92],"atoms.":[94],"This":[95],"approach":[96],"guarantees":[97],"fit":[101],"be":[103,107],"found":[104,216],"can":[106],"applied":[108],"even":[109],"when":[110],"sequence":[111],"similarity":[112],"low":[114],"or":[115],"does":[116],"not":[117],"exist":[118],"at":[119],"all.":[120],"have":[122,227],"implemented":[123],"in":[126,143,251],"Web":[128],"application":[129],"SiteBinder,":[130],"which":[131,149],"able":[133],"process":[135],"up":[136],"thousands":[138],"motifs":[142,244],"very":[145],"short":[146],"time,":[147],"an":[151],"intuitive":[152],"user-friendly":[154],"interface.":[155],"benchmarking":[157],"analysis":[158],"has":[159],"shown":[160],"robustness,":[162],"efficiency,":[163],"versatility":[165],"our":[167],"its":[170,225],"implementation":[171],"successful":[174],"1000":[177],"experimentally":[178],"determined":[179],"structures":[180,203],"each":[182],"32":[184],"eukaryotic":[185],"linear":[186],"also":[189],"demonstrate":[190],"applicability":[192],"SiteBinder":[194],"three":[196],"case":[197],"studies.":[198],"first":[200],"compared":[201],"61":[205],"PA-IIL":[206,223],"sugar":[207,219],"binding":[208,220,233],"sites":[209,221],"containing":[210],"nine":[211],"different":[212,234],"sugars,":[213],"we":[215,262],"mutants":[226],"conserved":[229],"structure":[230,250],"despite":[231],"their":[232],"sugars.":[235],"then":[237],"superimposed":[238,263],"over":[239],"300":[240],"zinc":[241],"finger":[242],"central":[243],"revealed":[246],"molecular":[249],"vicinity":[253],"Zn":[256],"highly":[259],"conserved.":[260],"Finally,":[261],"12":[264],"BH3":[265],"domains":[266],"pro-apoptotic":[268],"proteins.":[269],"findings":[271],"come":[272],"support":[274],"hypothesis":[276],"there":[278],"basis":[282],"functional":[285],"segregation":[286],"BH3-only":[288],"proteins":[289],"into":[290],"activators":[291],"enablers.":[293]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}