{"id":"https://openalex.org/W2395439412","doi":"https://doi.org/10.1021/acs.jcim.5b00210","title":"ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations","display_name":"ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations","publication_year":2015,"publication_date":"2015-06-22","ids":{"openalex":"https://openalex.org/W2395439412","doi":"https://doi.org/10.1021/acs.jcim.5b00210","mag":"2395439412","pmid":"https://pubmed.ncbi.nlm.nih.gov/26098831"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00210","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00210","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086310415","display_name":"Stefan Bietz","orcid":null},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stefan Bietz","raw_affiliation_strings":["University of Hamburg, Center for Bioinformatics (ZBH), Bundesstrasse 43, 20146 Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Hamburg, Center for Bioinformatics (ZBH), Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["University of Hamburg, Center for Bioinformatics (ZBH), Bundesstrasse 43, 20146 Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Hamburg, Center for Bioinformatics (ZBH), Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5083205378"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":null,"apc_paid":null,"fwci":1.5061,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.8292919,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"55","issue":"8","first_page":"1747","last_page":"1756"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996999979019165,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996999979019165,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9966999888420105,"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":0.9944000244140625,"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":0.5756376385688782},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5678750276565552},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5330204963684082},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.517331063747406},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5101621150970459},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.47813379764556885},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.4670271873474121},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4096587002277374},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3691227436065674},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35294824838638306},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25633594393730164},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1985989511013031},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1508485972881317},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.14720916748046875},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07948389649391174}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5756376385688782},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5678750276565552},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5330204963684082},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.517331063747406},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5101621150970459},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.47813379764556885},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4670271873474121},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4096587002277374},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3691227436065674},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35294824838638306},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25633594393730164},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1985989511013031},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1508485972881317},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.14720916748046875},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07948389649391174},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5b00210","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00210","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:26098831","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26098831","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2057840495","display_name":null,"funder_award_id":"KF2563701","funder_id":"https://openalex.org/F4320321469","funder_display_name":"Bundesministerium f\u00fcr Wirtschaft und Technologie"}],"funders":[{"id":"https://openalex.org/F4320321469","display_name":"Bundesministerium f\u00fcr Wirtschaft und Technologie","ror":"https://ror.org/02vgg2808"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1970707909","https://openalex.org/W1974422922","https://openalex.org/W1977173978","https://openalex.org/W1979147581","https://openalex.org/W1979414133","https://openalex.org/W1982441109","https://openalex.org/W1983194490","https://openalex.org/W1990137109","https://openalex.org/W2009658446","https://openalex.org/W2011632873","https://openalex.org/W2015848270","https://openalex.org/W2016219933","https://openalex.org/W2020040806","https://openalex.org/W2022058405","https://openalex.org/W2027687260","https://openalex.org/W2034215564","https://openalex.org/W2057019193","https://openalex.org/W2058987156","https://openalex.org/W2061305961","https://openalex.org/W2061799302","https://openalex.org/W2062884696","https://openalex.org/W2072180710","https://openalex.org/W2072351846","https://openalex.org/W2079153029","https://openalex.org/W2091708007","https://openalex.org/W2095302347","https://openalex.org/W2097612485","https://openalex.org/W2099432112","https://openalex.org/W2110397834","https://openalex.org/W2127067710","https://openalex.org/W2132629607","https://openalex.org/W2134878116","https://openalex.org/W2142801660","https://openalex.org/W2152326664","https://openalex.org/W2156825747","https://openalex.org/W2156909290","https://openalex.org/W2158957954","https://openalex.org/W2159590158","https://openalex.org/W2164088236","https://openalex.org/W2171371127","https://openalex.org/W4210388672","https://openalex.org/W4248107770"],"related_works":["https://openalex.org/W2029514038","https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W1985408726","https://openalex.org/W1482324242","https://openalex.org/W2088487249","https://openalex.org/W2187357871","https://openalex.org/W2141411672","https://openalex.org/W1981307089","https://openalex.org/W1741740882"],"abstract_inverted_index":{"The":[0],"usage":[1],"of":[2,12,65,69,83,122,142,171,193,214,239],"conformational":[3,132],"ensembles":[4],"constitutes":[5],"a":[6,93,97,165],"widespread":[7],"technique":[8],"for":[9,23,153,241],"the":[10,63,101,119,149,184,207,212],"consideration":[11],"protein":[13,45],"flexibility":[14],"in":[15,31,139,211],"computational":[16],"biology.":[17],"When":[18],"experimental":[19],"structures":[20,170,213,225],"are":[21,28],"applied":[22],"this":[24,134],"purpose,":[25],"alignment":[26,54,112,121,190],"techniques":[27],"usually":[29],"required":[30],"dealing":[32],"with":[33,221],"structural":[34,229],"deviations":[35],"and":[36,96,226,231],"annotation":[37],"inconsistencies.":[38],"Moreover,":[39],"many":[40],"application":[41],"scenarios":[42],"focus":[43],"on":[44,164],"ligand":[46],"binding":[47,72,89,185],"sites.":[48,73],"Here,":[49],"we":[50],"introduce":[51],"our":[52],"new":[53],"algorithm":[55],"ASCONA":[56,161,178,217,235],"that":[57,126],"has":[58],"been":[59,77],"specially":[60],"geared":[61],"to":[62,79,181,219,227],"problem":[64],"aligning":[66],"multiple":[67,88],"conformations":[68],"sequentially":[70],"similar":[71],"Intense":[74],"efforts":[75],"have":[76],"directed":[78],"an":[80,140,188],"accurate":[81],"detection":[82],"highly":[84,104,158,222],"flexible":[85,159],"backbone":[86,224],"deviations,":[87],"site":[90,186],"matches":[91,202],"within":[92],"single":[94],"structure,":[95],"reliable,":[98],"but":[99,145],"at":[100,187,244],"same":[102,208],"time":[103,144,192],"efficient,":[105],"search":[106],"algorithm.":[107],"In":[108,175],"contrast,":[109],"most":[110],"available":[111,237],"methods":[113],"rather":[114],"target":[115],"other":[116,215],"issues,":[117],"e.g.,":[118],"global":[120],"distantly":[123],"related":[124],"proteins":[125],"share":[127],"structurally":[128],"conserved":[129],"regions.":[130],"For":[131],"ensembles,":[133],"might":[135],"not":[136],"only":[137],"result":[138],"overhead":[141],"computation":[143,191],"could":[146],"also":[147],"affect":[148],"achieved":[150],"accuracy,":[151],"especially":[152],"more":[154],"complicated":[155],"cases":[156],"as":[157],"proteins.":[160,174,216],"was":[162,179],"evaluated":[163],"test":[166],"set":[167],"containing":[168],"1107":[169],"65":[172],"diverse":[173],"all":[176],"cases,":[177],"able":[180],"correctly":[182],"align":[183],"average":[189],"4":[194],"ms":[195],"per":[196],"target.":[197],"Furthermore,":[198],"no":[199],"false":[200],"positive":[201],"were":[203],"observed":[204],"when":[205],"searching":[206],"query":[209],"sites":[210],"proved":[218],"cope":[220],"deviating":[223],"tolerate":[228],"gaps":[230],"moderate":[232],"mutation":[233],"rates.":[234],"is":[236],"free":[238],"charge":[240],"academic":[242],"use":[243],"http://www.zbh.uni-hamburg.de/ascona":[245],".":[246]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
