{"id":"https://openalex.org/W4400024833","doi":"https://doi.org/10.1021/acs.jcim.5c01166","title":"General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design","display_name":"General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design","publication_year":2026,"publication_date":"2026-01-26","ids":{"openalex":"https://openalex.org/W4400024833","doi":"https://doi.org/10.1021/acs.jcim.5c01166","pmid":"https://pubmed.ncbi.nlm.nih.gov/41582456"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c01166","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01166","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":"preprint","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2406.16821","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Yue Jian","orcid":"https://orcid.org/0000-0003-2464-3337"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yue Jian","raw_affiliation_strings":["Department of Chemical & Biomolecular Engineering","University of California, Berkeley"],"raw_orcid":"https://orcid.org/0000-0003-2464-3337","affiliations":[{"raw_affiliation_string":"Department of Chemical & Biomolecular Engineering","institution_ids":[]},{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102629909","display_name":"Curtis Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Curtis Wu","raw_affiliation_strings":["Department of Chemistry","University of California, Berkeley"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032963060","display_name":"Danny Reidenbach","orcid":null},"institutions":[{"id":"https://openalex.org/I4210127875","display_name":"Nvidia (United States)","ror":"https://ror.org/03jdj4y14","country_code":"US","type":"company","lineage":["https://openalex.org/I4210127875"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Danny Reidenbach","raw_affiliation_strings":["NVIDIA Corporation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NVIDIA Corporation","institution_ids":["https://openalex.org/I4210127875"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049020441","display_name":"Aditi S. Krishnapriyan","orcid":"https://orcid.org/0000-0003-3472-6080"},"institutions":[{"id":"https://openalex.org/I4210116091","display_name":"Department of Physics, Mathematics and Informatics","ror":"https://ror.org/023sm4k53","country_code":"BY","type":"facility","lineage":["https://openalex.org/I151823869","https://openalex.org/I4210116091"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["BY","US"],"is_corresponding":false,"raw_author_name":"Aditi S. Krishnapriyan","raw_affiliation_strings":["Department of Chemical & Biomolecular Engineering","Department of Electrical Engineering & Computer Sciences","University of California, Berkeley"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical & Biomolecular Engineering","institution_ids":[]},{"raw_affiliation_string":"Department of Electrical Engineering & Computer Sciences","institution_ids":["https://openalex.org/I4210116091"]},{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":null,"apc_paid":null,"fwci":29.6913,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.97825291,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"66","issue":"3","first_page":"1342","last_page":"1352"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.987500011920929,"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":0.987500011920929,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9761999845504761,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9695000052452087,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"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/diffusion","display_name":"Diffusion","score":0.5547465682029724},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5333345532417297},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4466356635093689},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3420296311378479},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33489060401916504},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.21165049076080322},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.20314115285873413},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.18983066082000732},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.15329933166503906},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11413255333900452}],"concepts":[{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.5547465682029724},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5333345532417297},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4466356635093689},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3420296311378479},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33489060401916504},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.21165049076080322},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.20314115285873413},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.18983066082000732},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.15329933166503906},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11413255333900452}],"mesh":[{"descriptor_ui":"D004058","descriptor_name":"Diffusion","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":"D011485","descriptor_name":"Protein Binding","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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1021/acs.jcim.5c01166","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01166","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:41582456","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41582456","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},{"id":"pmh:oai:arXiv.org:2406.16821","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2406.16821","pdf_url":"https://arxiv.org/pdf/2406.16821","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"pmh:doi:10.48550/arxiv.2406.16821","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":"publisher-specific-oa","license_id":"https://openalex.org/licenses/publisher-specific-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"doi:10.48550/arxiv.2406.16821","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2406.16821","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2406.16821","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2406.16821","pdf_url":"https://arxiv.org/pdf/2406.16821","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7148947613","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337547","funder_display_name":"Laboratory Directed Research and Development"}],"funders":[{"id":"https://openalex.org/F4320337547","display_name":"Laboratory Directed Research and Development","ror":"https://ror.org/01e41cf67"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4400024833.pdf"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1975447903","https://openalex.org/W991789247","https://openalex.org/W2108389384","https://openalex.org/W2134967712","https://openalex.org/W2009423060","https://openalex.org/W4323650483","https://openalex.org/W4221149941","https://openalex.org/W4405463253","https://openalex.org/W3014154196","https://openalex.org/W4392822048","https://openalex.org/W4307416138","https://openalex.org/W3110257065","https://openalex.org/W3082411326","https://openalex.org/W1993046136","https://openalex.org/W2034549041","https://openalex.org/W2160592148","https://openalex.org/W4393100383","https://openalex.org/W4224311800","https://openalex.org/W4405194591","https://openalex.org/W2902812092","https://openalex.org/W4401066062","https://openalex.org/W3209764902","https://openalex.org/W4385889851"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"Structure-based":[0],"drug":[1,147],"design":[2,143],"(SBDD)":[3],"aims":[4],"to":[5,13,108,127,142],"generate":[6],"ligands":[7],"that":[8],"bind":[9],"strongly":[10],"and":[11,30,81,138,145],"specifically":[12],"target":[14],"protein":[15],"pockets.":[16],"Recent":[17],"diffusion":[18,54,91,129],"models":[19,55],"have":[20],"advanced":[21],"SBDD":[22],"by":[23,102],"capturing":[24],"the":[25,125],"distributions":[26],"of":[27,116],"atomic":[28],"positions":[29],"types,":[31],"yet":[32],"they":[33],"often":[34],"underemphasize":[35],"binding":[36,60,103,114,134],"affinity":[37,61,73,87,115],"control":[38],"during":[39,75],"generation.":[40],"To":[41],"address":[42],"this":[43],"limitation,":[44],"we":[45,123],"introduce":[46],"BADGER,":[47],"a":[48,78,109],"general":[49],"binding-affinity":[50],"guidance":[51],"framework":[52,126],"for":[53,133],"in":[56,77,112],"SBDD.":[57],"BADGER":[58,105],"incorporates":[59],"awareness":[62],"through":[63],"two":[64],"complementary":[65],"strategies:":[66],"(1)":[67],"classifier":[68],"guidance,":[69,84,130],"which":[70,85],"applies":[71],"gradient-based":[72],"signals":[74],"sampling":[76],"plug-and-play":[79],"fashion,":[80],"(2)":[82],"classifier-free":[83],"integrates":[86],"conditioning":[88],"directly":[89],"into":[90],"model":[92],"training.":[93],"Together,":[94],"these":[95],"approaches":[96],"enable":[97],"controllable":[98],"ligand":[99],"generation":[100],"guided":[101],"affinity.":[104],"achieves":[106],"up":[107],"60%":[110],"improvement":[111],"ligand-protein":[113],"sampled":[117],"molecules":[118],"over":[119],"prior":[120],"methods.":[121],"Furthermore,":[122],"extend":[124],"multiconstraint":[128],"jointly":[131],"optimizing":[132],"affinity,":[135],"drug-likeness":[136],"(QED),":[137],"synthetic":[139],"accessibility":[140],"(SA)":[141],"realistic":[144],"synthesizable":[146],"candidates.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-02-11T14:41:00.668223","created_date":"2024-06-26T00:00:00"}