{"id":"https://openalex.org/W2947285137","doi":"https://doi.org/10.1186/s13321-019-0358-3","title":"Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening","display_name":"Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening","publication_year":2019,"publication_date":"2019-05-24","ids":{"openalex":"https://openalex.org/W2947285137","doi":"https://doi.org/10.1186/s13321-019-0358-3","mag":"2947285137","pmid":"https://pubmed.ncbi.nlm.nih.gov/31127411"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-019-0358-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0358-3","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0358-3","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0358-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051881761","display_name":"Patrick J. Ropp","orcid":"https://orcid.org/0000-0002-9142-7557"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Patrick J. Ropp","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031636174","display_name":"Jacob O. Spiegel","orcid":"https://orcid.org/0000-0002-8496-6915"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob O. Spiegel","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103154997","display_name":"Jennifer L. Walker","orcid":"https://orcid.org/0000-0003-1220-1574"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer L. Walker","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021567178","display_name":"Harrison Green","orcid":"https://orcid.org/0000-0003-3986-3906"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harrison Green","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091208564","display_name":"Guillermo Morales","orcid":null},"institutions":[{"id":"https://openalex.org/I135191193","display_name":"University of Indianapolis","ror":"https://ror.org/052133d12","country_code":"US","type":"education","lineage":["https://openalex.org/I135191193"]},{"id":"https://openalex.org/I2802629803","display_name":"Innovate UK","ror":"https://ror.org/05ar5fy68","country_code":"GB","type":"government","lineage":["https://openalex.org/I2802629803","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Guillermo A. Morales","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA","Innoventyx, LLC, Oro Valley, AZ, 85737, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I135191193","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Innoventyx, LLC, Oro Valley, AZ, 85737, USA","institution_ids":["https://openalex.org/I2802629803"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003606293","display_name":"Katherine A. Milliken","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katherine A. Milliken","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051387369","display_name":"John J. Ringe","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John J. Ringe","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084976210","display_name":"Jacob D. Durrant","orcid":"https://orcid.org/0000-0002-5808-4097"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob D. Durrant","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA. durrantj@pitt.edu","Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA"],"raw_orcid":"https://orcid.org/0000-0002-5808-4097","affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA. durrantj@pitt.edu","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5051881761"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":7.6802,"has_fulltext":true,"cited_by_count":91,"citation_normalized_percentile":{"value":0.97743609,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"11","issue":"1","first_page":"34","last_page":"34"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.996999979019165,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9940999746322632,"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/virtual-screening","display_name":"Virtual screening","score":0.9331443309783936},{"id":"https://openalex.org/keywords/tautomer","display_name":"Tautomer","score":0.7305324673652649},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6787656545639038},{"id":"https://openalex.org/keywords/ring","display_name":"Ring (chemistry)","score":0.592682957649231},{"id":"https://openalex.org/keywords/gypsum","display_name":"Gypsum","score":0.5347745418548584},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5223687291145325},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.5025937557220459},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.4378352463245392},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.42845338582992554},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.40163373947143555},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.1576455533504486},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.14312535524368286},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.06955462694168091}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.9331443309783936},{"id":"https://openalex.org/C111233374","wikidata":"https://www.wikidata.org/wiki/Q334640","display_name":"Tautomer","level":2,"score":0.7305324673652649},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6787656545639038},{"id":"https://openalex.org/C2780378348","wikidata":"https://www.wikidata.org/wiki/Q25351438","display_name":"Ring (chemistry)","level":2,"score":0.592682957649231},{"id":"https://openalex.org/C2779229104","wikidata":"https://www.wikidata.org/wiki/Q82658","display_name":"Gypsum","level":2,"score":0.5347745418548584},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5223687291145325},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5025937557220459},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.4378352463245392},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.42845338582992554},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40163373947143555},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.1576455533504486},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.14312535524368286},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.06955462694168091},{"id":"https://openalex.org/C191897082","wikidata":"https://www.wikidata.org/wiki/Q11467","display_name":"Metallurgy","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":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-019-0358-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0358-3","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0358-3","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Cheminformatics","raw_type":"journal-article"},{"id":"pmid:31127411","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31127411","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:f0ffcaf375ed4762b1db353acca3ff86","is_oa":true,"landing_page_url":"https://doaj.org/article/f0ffcaf375ed4762b1db353acca3ff86","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 11, Iss 1, Pp 1-13 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6534830","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6534830","pdf_url":null,"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 Cheminform","raw_type":"Text"},{"id":"pmh:oai:scholarworks.indianapolis.iu.edu:1805/20489","is_oa":false,"landing_page_url":"https://hdl.handle.net/1805/20489","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PMC","raw_type":"Article"},{"id":"pmh:oai:scholarworks.iupui.edu:1805/20489","is_oa":true,"landing_page_url":"http://hdl.handle.net/1805/20489","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PMC","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/s13321-019-0358-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0358-3","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0358-3","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.550000011920929}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310174","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2947285137.pdf","grobid_xml":"https://content.openalex.org/works/W2947285137.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1970493581","https://openalex.org/W1977556410","https://openalex.org/W1980240737","https://openalex.org/W1992947643","https://openalex.org/W1993046136","https://openalex.org/W1995343013","https://openalex.org/W2001032894","https://openalex.org/W2008443909","https://openalex.org/W2010342533","https://openalex.org/W2012684279","https://openalex.org/W2019096255","https://openalex.org/W2030971064","https://openalex.org/W2031390939","https://openalex.org/W2047081177","https://openalex.org/W2053253524","https://openalex.org/W2059919683","https://openalex.org/W2072537419","https://openalex.org/W2078374001","https://openalex.org/W2086106287","https://openalex.org/W2086740184","https://openalex.org/W2090431249","https://openalex.org/W2092285329","https://openalex.org/W2100125011","https://openalex.org/W2105668062","https://openalex.org/W2106505086","https://openalex.org/W2130479394","https://openalex.org/W2134967712","https://openalex.org/W2140291772","https://openalex.org/W2146010526","https://openalex.org/W2150287412","https://openalex.org/W2161427213","https://openalex.org/W2169678694","https://openalex.org/W2244785476","https://openalex.org/W2531370029","https://openalex.org/W2606056265","https://openalex.org/W2609201554","https://openalex.org/W2755668533","https://openalex.org/W2902625972","https://openalex.org/W2920724574","https://openalex.org/W4285719527","https://openalex.org/W6610211995"],"related_works":["https://openalex.org/W2059230675","https://openalex.org/W2376003823","https://openalex.org/W2594726310","https://openalex.org/W2355193834","https://openalex.org/W2907597838","https://openalex.org/W2043558654","https://openalex.org/W2017996710","https://openalex.org/W4225792090","https://openalex.org/W2090863707","https://openalex.org/W4385741417"],"abstract_inverted_index":{"Computational":[0],"techniques":[1],"such":[2],"as":[3],"structure-based":[4],"virtual":[5,64,78,132],"screening":[6],"require":[7],"carefully":[8],"prepared":[9],"3D":[10,103],"models":[11],"of":[12,159,164],"potential":[13],"small-molecule":[14],"ligands.":[15],"Though":[16],"powerful,":[17],"existing":[18],"commercial":[19],"programs":[20],"for":[21,39],"virtual-library":[22],"preparation":[23],"have":[24],"restrictive":[25],"and/or":[26],"expensive":[27],"licenses.":[28],"Freely":[29],"available":[30,157],"alternatives,":[31],"though":[32],"often":[33],"effective,":[34],"do":[35],"not":[36],"fully":[37],"account":[38],"all":[40],"possible":[41],"ionization,":[42,83],"tautomeric,":[43,84],"and":[44,88,121],"ring-conformational":[45,89],"variants.":[46],"We":[47,134],"here":[48],"present":[49],"Gypsum-DL,":[50],"a":[51,126],"free,":[52],"robust":[53],"open-source":[54],"program":[55],"that":[56,147],"addresses":[57],"these":[58],"challenges.":[59],"As":[60,91],"input,":[61],"Gypsum-DL":[62,93,148,155],"accepts":[63],"compound":[65],"libraries":[66],"in":[67,76],"SMILES":[68],"or":[69],"flat":[70],"SDF":[71,96],"formats.":[72],"For":[73],"each":[74,99],"molecule":[75],"the":[77,116,142,162,165],"library,":[79],"it":[80],"enumerates":[81],"appropriate":[82],"chiral,":[85],"cis/trans":[86],"isomeric,":[87],"forms.":[90],"output,":[92],"produces":[94],"an":[95],"file":[97],"containing":[98],"molecular":[100],"form,":[101],"with":[102],"coordinates":[104],"assigned.":[105],"To":[106],"demonstrate":[107],"its":[108],"utility,":[109],"we":[110],"processed":[111],"1558":[112],"molecules":[113,123],"taken":[114,124],"from":[115,125,141],"NCI":[117],"Diversity":[118],"Set":[119],"VI":[120],"56,608":[122],"Distributed":[127],"Drug":[128],"Discovery":[129],"(D3)":[130],"combinatorial":[131],"library.":[133],"also":[135],"used":[136],"4463":[137],"high-quality":[138],"protein-ligand":[139],"complexes":[140],"PDBBind":[143],"database":[144],"to":[145],"show":[146],"processing":[149],"can":[150],"improve":[151],"virtual-screening":[152],"pose":[153],"prediction.":[154],"is":[156],"free":[158],"charge":[160],"under":[161],"terms":[163],"Apache":[166],"License,":[167],"Version":[168],"2.0.":[169]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
