{"id":"https://openalex.org/W4385381094","doi":"https://doi.org/10.1007/s10822-023-00522-4","title":"PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams","display_name":"PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams","publication_year":2023,"publication_date":"2023-07-29","ids":{"openalex":"https://openalex.org/W4385381094","doi":"https://doi.org/10.1007/s10822-023-00522-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/37515714"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-023-00522-4","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-023-00522-4","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-023-00522-4.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10822-023-00522-4.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039321558","display_name":"Konrad Diedrich","orcid":"https://orcid.org/0000-0001-8171-0888"},"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":"Konrad Diedrich","raw_affiliation_strings":["Universit\u00e4t Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany","Universit\u00e4t Hamburg, ZBH\u2014Center for Bioinformatics, 20146, Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH\u2014Center for Bioinformatics, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058288477","display_name":"Bennet Krause","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"]},{"id":"https://openalex.org/I18850439","display_name":"Capgemini (Netherlands)","ror":"https://ror.org/03amxdk57","country_code":"NL","type":"company","lineage":["https://openalex.org/I18850439","https://openalex.org/I4210136798"]}],"countries":["DE","NL"],"is_corresponding":false,"raw_author_name":"Bennet Krause","raw_affiliation_strings":["Capgemini, 10785, Berlin, Germany","Universit\u00e4t Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany","Universit\u00e4t Hamburg, ZBH\u2014Center for Bioinformatics, 20146, Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"Capgemini, 10785, Berlin, Germany","institution_ids":["https://openalex.org/I18850439"]},{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH\u2014Center for Bioinformatics, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092566662","display_name":"Ole Berg","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":"Ole Berg","raw_affiliation_strings":["Universit\u00e4t Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany","Universit\u00e4t Hamburg, ZBH\u2014Center for Bioinformatics, 20146, Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH\u2014Center for Bioinformatics, 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":false,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["Universit\u00e4t Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany. matthias.rarey@uni-hamburg.de","Universit\u00e4t Hamburg, ZBH\u2014Center for Bioinformatics, 20146, Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany. matthias.rarey@uni-hamburg.de","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH\u2014Center for Bioinformatics, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5039321558"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":{"value":2890,"currency":"EUR","value_usd":3690},"fwci":13.5324,"has_fulltext":true,"cited_by_count":88,"citation_normalized_percentile":{"value":0.99263437,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"37","issue":"10","first_page":"491","last_page":"503"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.998199999332428,"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"}},{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9736999869346619,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6988920569419861},{"id":"https://openalex.org/keywords/interactivity","display_name":"Interactivity","score":0.6838961243629456},{"id":"https://openalex.org/keywords/diagram","display_name":"Diagram","score":0.5548782348632812},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.543531060218811},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5396587252616882},{"id":"https://openalex.org/keywords/interaction-overview-diagram","display_name":"Interaction overview diagram","score":0.43489202857017517},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.368156760931015},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32690736651420593},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2223534882068634},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.19718948006629944},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.18418285250663757},{"id":"https://openalex.org/keywords/unified-modeling-language","display_name":"Unified Modeling Language","score":0.10839956998825073},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.08132368326187134}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6988920569419861},{"id":"https://openalex.org/C144430266","wikidata":"https://www.wikidata.org/wiki/Q839721","display_name":"Interactivity","level":2,"score":0.6838961243629456},{"id":"https://openalex.org/C186399060","wikidata":"https://www.wikidata.org/wiki/Q959962","display_name":"Diagram","level":2,"score":0.5548782348632812},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.543531060218811},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5396587252616882},{"id":"https://openalex.org/C68438427","wikidata":"https://www.wikidata.org/wiki/Q1665879","display_name":"Interaction overview diagram","level":4,"score":0.43489202857017517},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.368156760931015},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32690736651420593},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2223534882068634},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.19718948006629944},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.18418285250663757},{"id":"https://openalex.org/C145644426","wikidata":"https://www.wikidata.org/wiki/Q169411","display_name":"Unified Modeling Language","level":3,"score":0.10839956998825073},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.08132368326187134},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","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":"D003142","descriptor_name":"Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003142","descriptor_name":"Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003142","descriptor_name":"Communication","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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-023-00522-4","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-023-00522-4","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-023-00522-4.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:37515714","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37515714","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 computer-aided molecular design","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10440272","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10440272","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10440272/pdf/10822_2023_Article_522.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":"J Comput Aided Mol Des","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s10822-023-00522-4","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-023-00522-4","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-023-00522-4.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323381","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385381094.pdf"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W2037652830","https://openalex.org/W2039546043","https://openalex.org/W2043212464","https://openalex.org/W2069152576","https://openalex.org/W2074473216","https://openalex.org/W2081912151","https://openalex.org/W2100598991","https://openalex.org/W2123325078","https://openalex.org/W2130479394","https://openalex.org/W2145928638","https://openalex.org/W2151256267","https://openalex.org/W2167549547","https://openalex.org/W2582406409","https://openalex.org/W2586345785","https://openalex.org/W2610550630","https://openalex.org/W2779144909","https://openalex.org/W2806399642","https://openalex.org/W3016296419","https://openalex.org/W3046345744","https://openalex.org/W3177828909","https://openalex.org/W3197223249","https://openalex.org/W3203735717","https://openalex.org/W4225289163","https://openalex.org/W4367669413"],"related_works":["https://openalex.org/W3200046502","https://openalex.org/W98536524","https://openalex.org/W2061073323","https://openalex.org/W1925441854","https://openalex.org/W2186293198","https://openalex.org/W2982238776","https://openalex.org/W2347474403","https://openalex.org/W2767743462","https://openalex.org/W868084308","https://openalex.org/W2952519470"],"abstract_inverted_index":{"In":[0],"this":[1],"article,":[2],"we":[3],"present":[4],"PoseEdit,":[5,61],"a":[6,109],"new,":[7],"interactive":[8],"frontend":[9],"of":[10,23,60,87,113,119,126,144,153],"the":[11,56,62,70,91,117,142,175,191],"popular":[12],"pose":[13],"visualization":[14],"tool":[15],"PoseView.":[16],"PoseEdit":[17,107,154,186],"automatically":[18],"produces":[19],"high-quality":[20],"2D":[21,58,171],"diagrams":[22,42,63],"intermolecular":[24],"interactions":[25],"in":[26,33,46,51,90,178],"3D":[27],"binding":[28,166],"sites":[29],"calculated":[30],"from":[31,82],"ligands":[32],"complex":[34],"with":[35,75,159,174,180],"protein,":[36],"DNA,":[37],"and":[38,67,78,98,122,137,183],"RNA.":[39],"The":[40,124,150],"PoseView":[41],"have":[43],"been":[44],"improved":[45],"several":[47],"aspects,":[48],"most":[49],"notably":[50],"their":[52,131],"interactivity.":[53],"Thanks":[54],"to":[55,156,163],"easy-to-use":[57],"editor":[59],"are":[64],"extensively":[65],"editable":[66],"extendible":[68],"by":[69],"user,":[71],"can":[72,93,146],"be":[73,80,94,148],"merged":[74],"other":[76],"diagrams,":[77],"even":[79,103],"created":[81],"scratch.":[83],"A":[84],"large":[85],"variety":[86],"graphical":[88,139,170],"objects":[89,129],"diagram":[92,128],"moved,":[95],"rotated,":[96],"selected":[97],"highlighted,":[99],"mirrored,":[100],"removed,":[101],"or":[102],"newly":[104],"added.":[105],"Furthermore,":[106],"enables":[108],"synchronized":[110],"2D-3D":[111],"view":[112],"macromolecule-ligand":[114],"complexes":[115],"simplifying":[116],"analysis":[118],"structural":[120],"features":[121],"interactions.":[123],"representation":[125],"individual":[127,184],"regarding":[130],"visualized":[132],"chemical":[133],"properties,":[134],"like":[135,141],"stereochemistry,":[136],"general":[138],"styles,":[140],"color":[143],"interactions,":[145],"additionally":[147],"edited.":[149],"primary":[151],"objective":[152,181],"is":[155,187],"support":[157],"scientists":[158],"an":[160],"enhanced":[161],"way":[162],"communicate":[164],"ligand":[165],"mode":[167],"information":[168],"through":[169],"representations":[172],"optimized":[173],"scientist's":[176],"input":[177],"accordance":[179],"criteria":[182],"needs.":[185],"freely":[188],"available":[189],"on":[190],"ProteinsPlus":[192],"web":[193],"server":[194],"(":[195],"https://proteins.plus":[196],").":[197]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":32},{"year":2024,"cited_by_count":44},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-01T17:29:45.350535","created_date":"2025-10-10T00:00:00"}
