{"id":"https://openalex.org/W4410741943","doi":"https://doi.org/10.1186/s13321-025-01022-3","title":"Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations","display_name":"Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations","publication_year":2025,"publication_date":"2025-05-26","ids":{"openalex":"https://openalex.org/W4410741943","doi":"https://doi.org/10.1186/s13321-025-01022-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/40420238"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01022-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01022-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01022-3","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/counter/pdf/10.1186/s13321-025-01022-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003382143","display_name":"Alejandro Mart\u00ednez Le\u00f3n","orcid":null},"institutions":[{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alejandro Mart\u00ednez Le\u00f3n","raw_affiliation_strings":["Theoretical Physics and Center for Biophysics, Universit\u00e4t des Saarlandes, PharmaScienceHub (PSH), 66123, Saarbr\u00fccken, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Physics and Center for Biophysics, Universit\u00e4t des Saarlandes, PharmaScienceHub (PSH), 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I91712215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082893610","display_name":"Benjamin Ries","orcid":"https://orcid.org/0000-0002-0945-8304"},"institutions":[{"id":"https://openalex.org/I1330995197","display_name":"Boehringer Ingelheim (Germany)","ror":"https://ror.org/00q32j219","country_code":"DE","type":"company","lineage":["https://openalex.org/I1330995197"]},{"id":"https://openalex.org/I40695006","display_name":"Open Geospatial Consortium","ror":"https://ror.org/00fsdxs93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40695006"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Benjamin Ries","raw_affiliation_strings":["Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany","Open Molecular Software Foundation, Open Free Energy, Davis, CA, 95616, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany","institution_ids":["https://openalex.org/I1330995197"]},{"raw_affiliation_string":"Open Molecular Software Foundation, Open Free Energy, Davis, CA, 95616, USA","institution_ids":["https://openalex.org/I40695006"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068002595","display_name":"Jochen S. Hub","orcid":"https://orcid.org/0000-0001-7716-1767"},"institutions":[{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jochen S. Hub","raw_affiliation_strings":["Theoretical Physics and Center for Biophysics, Universit\u00e4t des Saarlandes, PharmaScienceHub (PSH), 66123, Saarbr\u00fccken, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Physics and Center for Biophysics, Universit\u00e4t des Saarlandes, PharmaScienceHub (PSH), 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I91712215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085408487","display_name":"Aniket Magarkar","orcid":"https://orcid.org/0000-0003-3385-964X"},"institutions":[{"id":"https://openalex.org/I1330995197","display_name":"Boehringer Ingelheim (Germany)","ror":"https://ror.org/00q32j219","country_code":"DE","type":"company","lineage":["https://openalex.org/I1330995197"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Aniket Magarkar","raw_affiliation_strings":["Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany. aniket.magarkar@boehringer-ingelheim.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany. aniket.magarkar@boehringer-ingelheim.com","institution_ids":["https://openalex.org/I1330995197"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11431396,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"85","last_page":"85"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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":0.9922999739646912,"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/T10274","display_name":"Synthesis and biological activity","score":0.9663000106811523,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6467213034629822},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6265350580215454},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.42033398151397705},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40793466567993164},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32688742876052856},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10249325633049011}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6467213034629822},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6265350580215454},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.42033398151397705},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40793466567993164},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32688742876052856},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10249325633049011}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01022-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01022-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01022-3","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:40420238","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40420238","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:0fb5ea7535c1432a809cc4f5934feecd","is_oa":true,"landing_page_url":"https://doaj.org/article/0fb5ea7535c1432a809cc4f5934feecd","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 17, Iss 1, Pp 1-22 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12107812","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12107812","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"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01022-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01022-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01022-3","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":[],"awards":[{"id":"https://openalex.org/G2464892713","display_name":null,"funder_award_id":"INST 256/539-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G3811267150","display_name":null,"funder_award_id":"256/539-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5923623626","display_name":null,"funder_award_id":"860592","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7146441415","display_name":null,"funder_award_id":"INST 256/ 539-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410741943.pdf","grobid_xml":"https://content.openalex.org/works/W4410741943.grobid-xml"},"referenced_works_count":90,"referenced_works":["https://openalex.org/W343086395","https://openalex.org/W1031578623","https://openalex.org/W1509196567","https://openalex.org/W1582109070","https://openalex.org/W1968098666","https://openalex.org/W1969189143","https://openalex.org/W1978222579","https://openalex.org/W1980581986","https://openalex.org/W1982792699","https://openalex.org/W1986176168","https://openalex.org/W1994859764","https://openalex.org/W2011230643","https://openalex.org/W2016156573","https://openalex.org/W2017792060","https://openalex.org/W2018604207","https://openalex.org/W2028629022","https://openalex.org/W2033016300","https://openalex.org/W2034549041","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2040521312","https://openalex.org/W2044834685","https://openalex.org/W2047399603","https://openalex.org/W2047819524","https://openalex.org/W2059013803","https://openalex.org/W2074140794","https://openalex.org/W2078521274","https://openalex.org/W2081693079","https://openalex.org/W2093755925","https://openalex.org/W2100627460","https://openalex.org/W2103034037","https://openalex.org/W2110791536","https://openalex.org/W2128572087","https://openalex.org/W2128824543","https://openalex.org/W2134967712","https://openalex.org/W2154670681","https://openalex.org/W2158534713","https://openalex.org/W2160592148","https://openalex.org/W2183050958","https://openalex.org/W2347697584","https://openalex.org/W2404280981","https://openalex.org/W2529996553","https://openalex.org/W2559603838","https://openalex.org/W2592262780","https://openalex.org/W2601243251","https://openalex.org/W2756333083","https://openalex.org/W2763220183","https://openalex.org/W2772606519","https://openalex.org/W2773987374","https://openalex.org/W2794774007","https://openalex.org/W2909063104","https://openalex.org/W2912171584","https://openalex.org/W2945999173","https://openalex.org/W2962764565","https://openalex.org/W3007133919","https://openalex.org/W3015608194","https://openalex.org/W3023600056","https://openalex.org/W3048079539","https://openalex.org/W3054319032","https://openalex.org/W3078129399","https://openalex.org/W3092297806","https://openalex.org/W3100751385","https://openalex.org/W3104830773","https://openalex.org/W3104956673","https://openalex.org/W3106761016","https://openalex.org/W3120361527","https://openalex.org/W3150635270","https://openalex.org/W3161725201","https://openalex.org/W3168436232","https://openalex.org/W3182055317","https://openalex.org/W3200806939","https://openalex.org/W3203735717","https://openalex.org/W4211218744","https://openalex.org/W4220823532","https://openalex.org/W4225835448","https://openalex.org/W4240713108","https://openalex.org/W4294991341","https://openalex.org/W4321784532","https://openalex.org/W4376226284","https://openalex.org/W4389396422","https://openalex.org/W4390886467","https://openalex.org/W4391637501","https://openalex.org/W4400245753","https://openalex.org/W4400834487","https://openalex.org/W4404115367","https://openalex.org/W4404755712","https://openalex.org/W4405194591","https://openalex.org/W6931515806","https://openalex.org/W6950516877","https://openalex.org/W6969257490"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Abstract":[0],"We":[1],"present":[2],"Moldrug,":[3,60],"a":[4,37,45,77,144],"computational":[5],"tool":[6],"for":[7,52,158,165],"accelerating":[8],"the":[9,18,26,53,67,99,148],"hit-to-lead":[10],"phase":[11],"in":[12],"structure-based":[13],"drug":[14],"design.":[15],"Moldrug":[16,40,56,140],"explores":[17],"chemical":[19,94],"space":[20],"using":[21,104],"structural":[22],"modifications":[23],"suggested":[24],"by":[25,30,43,75],"CReM":[27],"library":[28],"and":[29,47,86,106,172],"optimizing":[31,76],"an":[32],"adaptable":[33,164],"fitness":[34,79,156],"function":[35,80],"with":[36],"genetic":[38],"algorithm.":[39],"is":[41,141],"complemented":[42],"Moldrug-Dashboard,":[44],"cross-platform":[46],"user-friendly":[48],"graphical":[49],"interface":[50],"tailored":[51],"analysis":[54],"of":[55,73,98],"simulations.":[57],"To":[58],"illustrate":[59],"we":[61],"designed":[62,90,100],"new":[63],"potential":[64],"inhibitors":[65],"targeting":[66],"main":[68],"protease":[69],"(M":[70],"Pro":[71],")":[72],"SARS-CoV-2":[74],"consensus":[78],"that":[81],"balances":[82],"binding":[83,108],"affinity,":[84],"drug-likeness,":[85],"synthetic":[87],"accessibility.":[88],"The":[89],"molecules":[91,101],"exhibited":[92],"high":[93],"diversity.":[95],"A":[96],"subset":[97],"were":[102],"ranked":[103],"MM/GBSA":[105],"alchemical":[107],"free":[109],"energy":[110],"calculations,":[111],"revealing":[112],"predicted":[113],"affinities":[114],"as":[115,117,143],"low":[116],"$$-10\\,~\\hbox":[118],"{kcal}\\,\\hbox":[119],"{mol}^{-1}$$":[120],"<mml:math":[121],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">":[122],"<mml:mrow>":[123,132],"<mml:mo>-</mml:mo>":[124,133],"<mml:mn>10</mml:mn>":[125],"<mml:mspace/>":[126,127,129],"<mml:mtext>kcal</mml:mtext>":[128],"<mml:msup>":[130],"<mml:mtext>mol</mml:mtext>":[131],"<mml:mn>1</mml:mn>":[134],"</mml:mrow>":[135,137],"</mml:msup>":[136],"</mml:math>":[138],".":[139,178],"distributed":[142],"Python":[145],"package":[146],"under":[147],"Apache":[149],"2.0":[150],"license.":[151],"It":[152],"offers":[153],"pre-configured":[154],"multi-parameter":[155],"functions":[157],"molecular":[159],"design,":[160],"while":[161],"being":[162],"highly":[163],"integrating":[166],"functionalities":[167],"from":[168],"external":[169],"software.":[170],"Documentation":[171],"tutorials":[173],"are":[174],"available":[175],"at":[176],"https://moldrug.rtfd.io":[177]},"counts_by_year":[],"updated_date":"2026-06-20T22:02:38.213706","created_date":"2025-10-10T00:00:00"}