{"id":"https://openalex.org/W7132823045","doi":"https://doi.org/10.1021/acs.jcim.5c02921","title":"LigandExplorer: An Automated Tool for Ligand Extraction from PDB Structures","display_name":"LigandExplorer: An Automated Tool for Ligand Extraction from PDB Structures","publication_year":2026,"publication_date":"2026-02-28","ids":{"openalex":"https://openalex.org/W7132823045","doi":"https://doi.org/10.1021/acs.jcim.5c02921","pmid":"https://pubmed.ncbi.nlm.nih.gov/41762111"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02921","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02921","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/A5079643926","display_name":"Y. Li","orcid":null},"institutions":[{"id":"https://openalex.org/I173759888","display_name":"Hunan Normal University","ror":"https://ror.org/053w1zy07","country_code":"CN","type":"education","lineage":["https://openalex.org/I173759888"]},{"id":"https://openalex.org/I4210105641","display_name":"Peptide Protein Research (United Kingdom)","ror":"https://ror.org/01e8xap89","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210105641"]},{"id":"https://openalex.org/I4210105962","display_name":"Recombinant Antibody Technology (United Kingdom)","ror":"https://ror.org/01tmhf693","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210105962"]},{"id":"https://openalex.org/I4210151276","display_name":"Peptide Institute (Japan)","ror":"https://ror.org/055bszj51","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210151276"]}],"countries":["CN","GB","JP"],"is_corresponding":false,"raw_author_name":"Yaqi Li","raw_affiliation_strings":["Atombeat Technology Pte. Ltd., 6 Rafflesr Quay 048580, Singapore","College of Life Sciences, Hunan Normal University","Hunan Normal University","Institute of Interdisciplinary Studies","Peptide and small molecule drug R&D platform, Furong Laboratory","The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development"],"raw_orcid":"https://orcid.org/0000-0002-3010-2599","affiliations":[{"raw_affiliation_string":"Atombeat Technology Pte. Ltd., 6 Rafflesr Quay 048580, Singapore","institution_ids":["https://openalex.org/I4210105962"]},{"raw_affiliation_string":"College of Life Sciences, Hunan Normal University","institution_ids":["https://openalex.org/I173759888"]},{"raw_affiliation_string":"Hunan Normal University","institution_ids":["https://openalex.org/I173759888"]},{"raw_affiliation_string":"Institute of Interdisciplinary Studies","institution_ids":[]},{"raw_affiliation_string":"Peptide and small molecule drug R&D platform, Furong Laboratory","institution_ids":["https://openalex.org/I4210105641"]},{"raw_affiliation_string":"The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development","institution_ids":["https://openalex.org/I4210151276"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037733828","display_name":"Rongfeng Zou","orcid":"https://orcid.org/0000-0003-1988-7898"},"institutions":[{"id":"https://openalex.org/I4210105962","display_name":"Recombinant Antibody Technology (United Kingdom)","ror":"https://ror.org/01tmhf693","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210105962"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rongfeng Zou","raw_affiliation_strings":["Atombeat Technology Pte. Ltd., 6 Rafflesr Quay 048580, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atombeat Technology Pte. Ltd., 6 Rafflesr Quay 048580, Singapore","institution_ids":["https://openalex.org/I4210105962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5127490304","display_name":"Maohua Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105962","display_name":"Recombinant Antibody Technology (United Kingdom)","ror":"https://ror.org/01tmhf693","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210105962"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Maohua Yang","raw_affiliation_strings":["Atombeat Technology Pte. Ltd., 6 Rafflesr Quay 048580, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atombeat Technology Pte. Ltd., 6 Rafflesr Quay 048580, Singapore","institution_ids":["https://openalex.org/I4210105962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124091797","display_name":"Ying Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I173759888","display_name":"Hunan Normal University","ror":"https://ror.org/053w1zy07","country_code":"CN","type":"education","lineage":["https://openalex.org/I173759888"]},{"id":"https://openalex.org/I4210105641","display_name":"Peptide Protein Research (United Kingdom)","ror":"https://ror.org/01e8xap89","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210105641"]},{"id":"https://openalex.org/I4210151276","display_name":"Peptide Institute (Japan)","ror":"https://ror.org/055bszj51","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210151276"]}],"countries":["CN","GB","JP"],"is_corresponding":true,"raw_author_name":"Ying Wang","raw_affiliation_strings":["College of Life Sciences, Hunan Normal University","Hunan Normal University","Institute of Interdisciplinary Studies","Peptide and small molecule drug R&D platform, Furong Laboratory","The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development"],"raw_orcid":"https://orcid.org/0000-0002-4359-3753","affiliations":[{"raw_affiliation_string":"College of Life Sciences, Hunan Normal University","institution_ids":["https://openalex.org/I173759888"]},{"raw_affiliation_string":"Hunan Normal University","institution_ids":["https://openalex.org/I173759888"]},{"raw_affiliation_string":"Institute of Interdisciplinary Studies","institution_ids":[]},{"raw_affiliation_string":"Peptide and small molecule drug R&D platform, Furong Laboratory","institution_ids":["https://openalex.org/I4210105641"]},{"raw_affiliation_string":"The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development","institution_ids":["https://openalex.org/I4210151276"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhonghua Liu","orcid":"https://orcid.org/0000-0001-8497-6702"},"institutions":[{"id":"https://openalex.org/I173759888","display_name":"Hunan Normal University","ror":"https://ror.org/053w1zy07","country_code":"CN","type":"education","lineage":["https://openalex.org/I173759888"]},{"id":"https://openalex.org/I4210105641","display_name":"Peptide Protein Research (United Kingdom)","ror":"https://ror.org/01e8xap89","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210105641"]},{"id":"https://openalex.org/I4210151276","display_name":"Peptide Institute (Japan)","ror":"https://ror.org/055bszj51","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210151276"]}],"countries":["CN","GB","JP"],"is_corresponding":true,"raw_author_name":"Zhonghua Liu","raw_affiliation_strings":["College of Life Sciences, Hunan Normal University","Hunan Normal University","Institute of Interdisciplinary Studies","Peptide and small molecule drug R&D platform, Furong Laboratory","The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development"],"raw_orcid":"https://orcid.org/0000-0001-8497-6702","affiliations":[{"raw_affiliation_string":"College of Life Sciences, Hunan Normal University","institution_ids":["https://openalex.org/I173759888"]},{"raw_affiliation_string":"Hunan Normal University","institution_ids":["https://openalex.org/I173759888"]},{"raw_affiliation_string":"Institute of Interdisciplinary Studies","institution_ids":[]},{"raw_affiliation_string":"Peptide and small molecule drug R&D platform, Furong Laboratory","institution_ids":["https://openalex.org/I4210105641"]},{"raw_affiliation_string":"The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development","institution_ids":["https://openalex.org/I4210151276"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5127525802","display_name":"Hang Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105962","display_name":"Recombinant Antibody Technology (United Kingdom)","ror":"https://ror.org/01tmhf693","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210105962"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Hang Zheng","raw_affiliation_strings":["Atombeat Technology Pte. Ltd., 6 Rafflesr Quay 048580, Singapore"],"raw_orcid":"https://orcid.org/0000-0002-2825-0576","affiliations":[{"raw_affiliation_string":"Atombeat Technology Pte. Ltd., 6 Rafflesr Quay 048580, Singapore","institution_ids":["https://openalex.org/I4210105962"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5124091797","https://openalex.org/A5127525802"],"corresponding_institution_ids":["https://openalex.org/I173759888","https://openalex.org/I4210105641","https://openalex.org/I4210105962","https://openalex.org/I4210151276"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.31178471,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"6","first_page":"3026","last_page":"3035"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8126000165939331,"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":0.8126000165939331,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.048500001430511475,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.031700000166893005,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7860000133514404},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.6262999773025513},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.5026000142097473},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.4810999929904938},{"id":"https://openalex.org/keywords/downstream","display_name":"Downstream (manufacturing)","score":0.43059998750686646},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4138999879360199},{"id":"https://openalex.org/keywords/upstream","display_name":"Upstream (networking)","score":0.3382999897003174},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.3257000148296356}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7860000133514404},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6937000155448914},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.6262999773025513},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.61080002784729},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.5026000142097473},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.4810999929904938},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.43059998750686646},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4138999879360199},{"id":"https://openalex.org/C191172861","wikidata":"https://www.wikidata.org/wiki/Q7899321","display_name":"Upstream (networking)","level":2,"score":0.3382999897003174},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33660000562667847},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3257000148296356},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.31619998812675476},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.31610000133514404},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.3158999979496002},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.3086000084877014},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.30660000443458557},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.3034000098705292},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.2946000099182129},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.29179999232292175},{"id":"https://openalex.org/C125832229","wikidata":"https://www.wikidata.org/wiki/Q6503924","display_name":"Chemical nomenclature","level":2,"score":0.2822999954223633},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.28029999136924744},{"id":"https://openalex.org/C3019060180","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automated method","level":2,"score":0.2671999931335449},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.26579999923706055},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.26460000872612},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.25839999318122864},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.25189998745918274}],"mesh":[{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","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":"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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":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":"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":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c02921","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02921","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:41762111","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41762111","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":[{"id":"https://metadata.un.org/sdg/9","score":0.4027514159679413,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1048550002","display_name":null,"funder_award_id":"22473041","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1678468913","display_name":null,"funder_award_id":"2024JJ2042","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"},{"id":"https://openalex.org/G2991832869","display_name":null,"funder_award_id":"23A0084","funder_id":"https://openalex.org/F4320333642","funder_display_name":"Scientific Research Foundation of Hunan Provincial Education Department"},{"id":"https://openalex.org/G8028728988","display_name":null,"funder_award_id":"32171271","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322843","display_name":"Natural Science Foundation of\u00a0Hunan Province","ror":null},{"id":"https://openalex.org/F4320333642","display_name":"Scientific Research Foundation of Hunan Provincial Education Department","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1969017960","https://openalex.org/W1993403967","https://openalex.org/W1995808589","https://openalex.org/W2009388678","https://openalex.org/W2018661561","https://openalex.org/W2074222872","https://openalex.org/W2077870722","https://openalex.org/W2079453672","https://openalex.org/W2092285329","https://openalex.org/W2097035920","https://openalex.org/W2097836986","https://openalex.org/W2098432123","https://openalex.org/W2114162221","https://openalex.org/W2123822641","https://openalex.org/W2130479394","https://openalex.org/W2132022337","https://openalex.org/W2137841449","https://openalex.org/W2137923055","https://openalex.org/W2140036600","https://openalex.org/W2144440706","https://openalex.org/W2146465875","https://openalex.org/W2587598315","https://openalex.org/W2621473099","https://openalex.org/W2752727929","https://openalex.org/W2874062053","https://openalex.org/W3093634533","https://openalex.org/W3159177617","https://openalex.org/W4200139236","https://openalex.org/W4252171081","https://openalex.org/W4298128332","https://openalex.org/W4321611538","https://openalex.org/W4322008907","https://openalex.org/W4367040840","https://openalex.org/W4367049415","https://openalex.org/W4385407166","https://openalex.org/W4389836921","https://openalex.org/W4390049362","https://openalex.org/W4390578919","https://openalex.org/W4391426452","https://openalex.org/W4396721167","https://openalex.org/W4396789292","https://openalex.org/W4402273478"],"related_works":[],"abstract_inverted_index":{"The":[0],"structural":[1,130],"information":[2],"on":[3],"protein\u2013ligand":[4],"complexes":[5],"is":[6,68,97],"crucial":[7],"for":[8,56,202],"small-molecule":[9],"design":[10],"and":[11,25,43,46,53,75,88,90,147,156,195,205],"drug":[12],"discovery.":[13],"Yet":[14],"primary":[15,187],"resources":[16],"often":[17],"have":[18],"heterogeneous":[19],"annotations,":[20],"lack":[21],"machine-ready":[22],"ligand":[23],"categorization,":[24],"require":[26],"substantial":[27],"postprocessing":[28,39],"before":[29],"large-scale":[30],"modeling.":[31],"Here,":[32],"we":[33],"present":[34],"LigandExplorer,":[35],"an":[36],"open-source,":[37],"automated":[38],"pipeline":[40,96],"that":[41],"identifies":[42],"extracts":[44],"covalent":[45],"noncovalent":[47],"ligands":[48,81],"from":[49,64],"biomolecular":[50],"complex":[51,182],"structures":[52],"standardizes":[54],"outputs":[55],"downstream":[57],"use.":[58],"Using":[59],"residue-level":[60],"graphs":[61],"built":[62],"solely":[63],"atomic":[65],"coordinates,":[66],"LigandExplorer":[67,125,163,190],"robust":[69],"to":[70,79,103,108,137],"missing":[71],"or":[72],"inconsistent":[73],"metadata":[74],"integrates":[76],"LightGBM":[77],"models":[78],"classify":[80],"(peptides,":[82],"nucleic":[83],"acids,":[84],"phospholipids,":[85],"carbohydrates,":[86],"organics,":[87],"ions)":[89],"assess":[91],"interaction":[92],"relevance.":[93],"Because":[94],"the":[95,120,141,161,186],"rerunnable,":[98],"it":[99],"can":[100],"be":[101],"applied":[102],"each":[104],"new":[105],"databases":[106],"release":[107],"keep":[109],"derived,":[110],"categorized":[111],"data":[112,200],"sets":[113,201],"current":[114],"without":[115],"altering":[116],"source":[117],"records.":[118,159],"On":[119,160],"PDBbind":[121],"v2020":[122],"refined":[123],"set,":[124],"achieved":[126],"a":[127,171],"98.38%":[128],"raw":[129,153],"agreement":[131],"under":[132],"harmonized":[133],"comparison":[134],"criteria":[135],"prior":[136],"any":[138],"manual":[139],"reconciliation;":[140],"remaining":[142],"discrepancies":[143],"were":[144,148],"analyzed":[145],"separately":[146],"dominated":[149],"by":[150],"divergences":[151],"between":[152],"RCSB":[154],"entries":[155],"curated":[157],"PDBBind":[158],"PepBDB,":[162],"successfully":[164],"processed":[165],"4881":[166],"of":[167],"5005":[168],"complexes,":[169],"achieving":[170],"97.52%":[172],"success":[173],"rate.":[174],"Most":[175],"failures":[176],"reflected":[177],"upstream":[178],"record":[179],"errors,":[180],"where":[181],"cyclic":[183],"peptides":[184],"constituted":[185],"algorithmic":[188],"boundary.":[189],"thus":[191],"mitigates":[192],"data-cleaning":[193],"burdens":[194],"enables":[196],"rapidly":[197],"refreshed,":[198],"standardized":[199],"computational":[203],"modeling":[204],"molecular":[206],"design.":[207]},"counts_by_year":[],"updated_date":"2026-06-13T07:54:00.901334","created_date":"2026-03-01T00:00:00"}