{"id":"https://openalex.org/W4405028620","doi":"https://doi.org/10.1007/s10822-024-00581-1","title":"Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays","display_name":"Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays","publication_year":2024,"publication_date":"2024-12-04","ids":{"openalex":"https://openalex.org/W4405028620","doi":"https://doi.org/10.1007/s10822-024-00581-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/39630291"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-024-00581-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-024-00581-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-024-00581-1.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/s10822-024-00581-1.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060841618","display_name":"Sophia M. N. H\u00f6nig","orcid":"https://orcid.org/0000-0003-4742-7899"},"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":"Sophia M. N. H\u00f6nig","raw_affiliation_strings":["BioSolveIT, An der Ziegelei 79, 53757, Sankt Augustin, Germany","University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4742-7899","affiliations":[{"raw_affiliation_string":"BioSolveIT, An der Ziegelei 79, 53757, Sankt Augustin, Germany","institution_ids":[]},{"raw_affiliation_string":"University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045638100","display_name":"Torben Gutermuth","orcid":"https://orcid.org/0000-0002-9304-8251"},"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":"Torben Gutermuth","raw_affiliation_strings":["University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9304-8251","affiliations":[{"raw_affiliation_string":"University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052764114","display_name":"Christiane Ehrt","orcid":"https://orcid.org/0000-0003-1428-0042"},"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":"Christiane Ehrt","raw_affiliation_strings":["University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1428-0042","affiliations":[{"raw_affiliation_string":"University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087574034","display_name":"Christian Lemmen","orcid":"https://orcid.org/0000-0002-4264-6657"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christian Lemmen","raw_affiliation_strings":["BioSolveIT, An der Ziegelei 79, 53757, Sankt Augustin, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4264-6657","affiliations":[{"raw_affiliation_string":"BioSolveIT, An der Ziegelei 79, 53757, Sankt Augustin, Germany","institution_ids":[]}]},{"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, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany. matthias.rarey@uni-hamburg.de"],"raw_orcid":"https://orcid.org/0000-0002-9553-6531","affiliations":[{"raw_affiliation_string":"University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany. matthias.rarey@uni-hamburg.de","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5083205378"],"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":0.319,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.6503938,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"39","issue":"1","first_page":"2","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9929999709129333,"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":0.9884999990463257,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.602691113948822},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5750448703765869},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.547663688659668},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5431633591651917},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.537259042263031},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5016014575958252},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.4988985061645508},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4816505014896393},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.4267337918281555},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40486931800842285},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33293938636779785},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29364991188049316},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.221003919839859}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.602691113948822},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5750448703765869},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.547663688659668},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5431633591651917},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.537259042263031},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5016014575958252},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.4988985061645508},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4816505014896393},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.4267337918281555},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40486931800842285},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33293938636779785},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29364991188049316},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.221003919839859},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"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/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"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":"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":"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","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":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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-024-00581-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-024-00581-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-024-00581-1.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:39630291","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39630291","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:11618164","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11618164","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11618164/pdf/10822_2024_Article_581.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/s10822-024-00581-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-024-00581-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-024-00581-1.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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405028620.pdf","grobid_xml":"https://content.openalex.org/works/W4405028620.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W959778778","https://openalex.org/W1491938055","https://openalex.org/W1596324297","https://openalex.org/W1605711358","https://openalex.org/W1707232238","https://openalex.org/W1835740130","https://openalex.org/W1965957440","https://openalex.org/W1966851745","https://openalex.org/W1966950894","https://openalex.org/W1968319881","https://openalex.org/W1971458166","https://openalex.org/W1972190210","https://openalex.org/W1975875968","https://openalex.org/W1979914800","https://openalex.org/W1980880280","https://openalex.org/W1982797808","https://openalex.org/W1984261657","https://openalex.org/W1993046136","https://openalex.org/W2000061529","https://openalex.org/W2004467401","https://openalex.org/W2010099233","https://openalex.org/W2011953761","https://openalex.org/W2027065525","https://openalex.org/W2035585923","https://openalex.org/W2037167896","https://openalex.org/W2038361288","https://openalex.org/W2046037068","https://openalex.org/W2057350662","https://openalex.org/W2092285329","https://openalex.org/W2105649494","https://openalex.org/W2106605095","https://openalex.org/W2108236403","https://openalex.org/W2127648442","https://openalex.org/W2127760066","https://openalex.org/W2130479394","https://openalex.org/W2144659448","https://openalex.org/W2170146596","https://openalex.org/W2204695023","https://openalex.org/W2238707319","https://openalex.org/W2551556495","https://openalex.org/W2569093964","https://openalex.org/W2587816047","https://openalex.org/W2749017887","https://openalex.org/W2763443264","https://openalex.org/W2887475976","https://openalex.org/W2891800472","https://openalex.org/W2955791106","https://openalex.org/W3037466704","https://openalex.org/W3093450407","https://openalex.org/W3095583226","https://openalex.org/W3118317455","https://openalex.org/W3163511095","https://openalex.org/W4248107770","https://openalex.org/W4304183271","https://openalex.org/W4389900027","https://openalex.org/W4392576471"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"Although":[0],"small":[1],"molecule":[2],"superposition":[3,150,263],"is":[4,19,235],"a":[5,11,44,73,78,203,242],"standard":[6],"technique":[7],"in":[8,23,72],"drug":[9],"discovery,":[10],"rigorous":[12],"performance":[13,229],"assessment":[14],"of":[15,142,146,157,187,205],"the":[16,70,93,96,126,140,154,158,162,188,194],"corresponding":[17],"methods":[18],"currently":[20],"challenging.":[21],"Datasets":[22],"this":[24],"field":[25],"are":[26,98,251],"sparse,":[27],"small,":[28],"tailored":[29],"to":[30,101],"specific":[31],"applications,":[32],"unavailable,":[33],"or":[34,226,261],"outdated.":[35],"The":[36,199,232,248],"newly":[37],"developed":[38],"LOBSTER":[39,55,200,233],"set":[40,201,234],"described":[41],"herein":[42],"offers":[43,202],"publicly":[45,236],"available":[46,237,252],"and":[47,52,107,176,217,244,257],"method-independent":[48],"dataset":[49,163],"for":[50,57,139,148,182,220,259],"benchmarking":[51,208],"method":[53],"optimization.":[54],"stands":[56],"\"Ligand":[58],"Overlays":[59],"from":[60,69,117],"Binding":[61],"SiTe":[62],"Ensemble":[63],"Representatives\".":[64],"All":[65],"ligands":[66,94,116],"were":[67,85,128],"derived":[68],"PDB":[71],"fully":[74],"automated":[75],"workflow,":[76],"including":[77],"ligand":[79,83,112,122],"efficiency":[80],"filter.":[81],"So-called":[82],"ensembles":[84,97,113,127],"assembled":[86],"by":[87],"aligning":[88],"identical":[89],"binding":[90,105],"sites.":[91],"Thus,":[92],"within":[95,196],"superimposed":[99],"according":[100],"their":[102,136],"experimentally":[103],"determined":[104],"orientation":[106],"conformation.":[108],"Overall,":[109],"671":[110],"representative":[111],"comprise":[114],"3583":[115],"3521":[118],"proteins.":[119],"Altogether,":[120],"72,734":[121],"pairs":[123],"based":[124,134,222],"on":[125,135,153,223],"grouped":[129],"into":[130],"ten":[131],"distinct":[132],"subsets":[133],"volume":[137],"overlap,":[138],"benefit":[141],"introducing":[143],"different":[144,266],"degrees":[145],"difficulty":[147],"evaluating":[149],"methods.":[151],"Statistics":[152],"physicochemical":[155],"properties":[156],"compounds":[159],"indicate":[160],"that":[161],"represents":[164],"drug-like":[165],"compounds.":[166],"Consensus":[167],"Diversity":[168],"Plots":[169],"show":[170],"predominantly":[171],"high":[172],"Bemis-Murcko":[173],"scaffold":[174],"diversity":[175],"low":[177],"median":[178],"MACCS":[179],"fingerprint":[180],"similarity":[181],"each":[183],"ensemble.":[184],"An":[185],"analysis":[186],"underlying":[189],"protein":[190],"classes":[191],"further":[192],"demonstrates":[193],"heterogeneity":[195],"our":[197],"dataset.":[198],"variety":[204],"applications":[206],"like":[207],"multiple":[209],"as":[210,212],"well":[211],"pairwise":[213],"alignments,":[214],"generating":[215],"training":[216],"test":[218],"sets,":[219],"example":[221],"time":[224],"splits,":[225],"empirical":[227],"software":[228],"evaluation":[230],"studies.":[231],"at":[238,253],"https://doi.org/10.5281/zenodo.12658320":[239],",":[240,255],"representing":[241],"stable":[243],"versioned":[245],"data":[246,267],"resource.":[247],"Python":[249],"scripts":[250],"https://github.com/rareylab/LOBSTER":[254],"open-source,":[256],"allow":[258],"updating":[260],"recreating":[262],"sets":[264],"with":[265],"sources.":[268]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-13T06:13:01.061226","created_date":"2025-10-10T00:00:00"}