{"id":"https://openalex.org/W4413107181","doi":"https://doi.org/10.1371/journal.pcbi.1013367","title":"Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics","display_name":"Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics","publication_year":2025,"publication_date":"2025-08-11","ids":{"openalex":"https://openalex.org/W4413107181","doi":"https://doi.org/10.1371/journal.pcbi.1013367","pmid":"https://pubmed.ncbi.nlm.nih.gov/40788932"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013367","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013367","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013367","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082899961","display_name":"Nandan Haloi","orcid":"https://orcid.org/0000-0003-3542-333X"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Nandan Haloi","raw_affiliation_strings":["Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden"],"raw_orcid":"https://orcid.org/0000-0003-3542-333X","affiliations":[{"raw_affiliation_string":"Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I86987016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050363304","display_name":"Rebecca J. Howard","orcid":"https://orcid.org/0000-0001-7264-4364"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Rebecca J. Howard","raw_affiliation_strings":["Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden","Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I86987016"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008875190","display_name":"Erik Lindahl","orcid":"https://orcid.org/0000-0002-2734-2794"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Erik Lindahl","raw_affiliation_strings":["Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden","Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-2734-2794","affiliations":[{"raw_affiliation_string":"Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I86987016"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5008875190","https://openalex.org/A5050363304","https://openalex.org/A5082899961"],"corresponding_institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495","https://openalex.org/I86987016"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.5512,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.90952588,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"21","issue":"8","first_page":"e1013367","last_page":"e1013367"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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"}},"topics":[{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T11162","display_name":"Enzyme Structure and Function","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9965000152587891,"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/ligand","display_name":"Ligand (biochemistry)","score":0.5814193487167358},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.47809264063835144},{"id":"https://openalex.org/keywords/cryo-electron-microscopy","display_name":"Cryo-electron microscopy","score":0.4724726378917694},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.46292945742607117},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44992318749427795},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44142797589302063},{"id":"https://openalex.org/keywords/resolution","display_name":"Resolution (logic)","score":0.4407186508178711},{"id":"https://openalex.org/keywords/biomolecule","display_name":"Biomolecule","score":0.41844186186790466},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.403395414352417},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32206273078918457},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.3079298436641693},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.2845311760902405},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.274554967880249},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22767838835716248},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.21219107508659363},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.16639026999473572},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10502132773399353}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5814193487167358},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.47809264063835144},{"id":"https://openalex.org/C20702342","wikidata":"https://www.wikidata.org/wiki/Q5190506","display_name":"Cryo-electron microscopy","level":2,"score":0.4724726378917694},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.46292945742607117},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44992318749427795},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44142797589302063},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.4407186508178711},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.41844186186790466},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.403395414352417},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32206273078918457},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.3079298436641693},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.2845311760902405},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.274554967880249},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22767838835716248},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.21219107508659363},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.16639026999473572},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10502132773399353},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[{"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":"D011485","descriptor_name":"Protein Binding","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"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":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013367","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013367","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40788932","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40788932","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:c2ac38b1272f414f9c8a6b4602560902","is_oa":true,"landing_page_url":"https://doaj.org/article/c2ac38b1272f414f9c8a6b4602560902","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":"PLoS Computational Biology, Vol 21, Iss 8, p e1013367 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12364316","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12364316","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013367","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013367","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2117197532","display_name":null,"funder_award_id":"2019-02433","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G6481367159","display_name":"Characterizing ligand-protein interactions with a cryo-EM data-driven modeling approach","funder_award_id":"101107036","funder_id":"https://openalex.org/F4320338438","funder_display_name":"HORIZON EUROPE Marie Sklodowska-Curie Actions"},{"id":"https://openalex.org/G8099961586","display_name":null,"funder_award_id":"2021-05806","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G8104330905","display_name":null,"funder_award_id":"2023.0254","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"}],"funders":[{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320338438","display_name":"HORIZON EUROPE Marie Sklodowska-Curie Actions","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W63074263","https://openalex.org/W1972403093","https://openalex.org/W1976499671","https://openalex.org/W2020386906","https://openalex.org/W2021520922","https://openalex.org/W2029667189","https://openalex.org/W2034549041","https://openalex.org/W2057477511","https://openalex.org/W2067174909","https://openalex.org/W2070753604","https://openalex.org/W2076385318","https://openalex.org/W2129172946","https://openalex.org/W2140574901","https://openalex.org/W2469449201","https://openalex.org/W2555870966","https://openalex.org/W2744377419","https://openalex.org/W2799415291","https://openalex.org/W2918297620","https://openalex.org/W2953798760","https://openalex.org/W2994850615","https://openalex.org/W3012682588","https://openalex.org/W3024617926","https://openalex.org/W3025134193","https://openalex.org/W3035076119","https://openalex.org/W3035762603","https://openalex.org/W3082691473","https://openalex.org/W3083859380","https://openalex.org/W3090716937","https://openalex.org/W3092054218","https://openalex.org/W3102022293","https://openalex.org/W4307802116","https://openalex.org/W4308430063","https://openalex.org/W4308768440","https://openalex.org/W4322733414","https://openalex.org/W4379470910","https://openalex.org/W4381612882","https://openalex.org/W4385410521","https://openalex.org/W4386505414","https://openalex.org/W4386944943","https://openalex.org/W4387164156","https://openalex.org/W4389233086","https://openalex.org/W4389480950","https://openalex.org/W4390393899","https://openalex.org/W4390499518","https://openalex.org/W4392959216","https://openalex.org/W4392980203","https://openalex.org/W4394577549","https://openalex.org/W4396721167","https://openalex.org/W4400795417","https://openalex.org/W4400949307","https://openalex.org/W4401844424","https://openalex.org/W4403318777","https://openalex.org/W4403324307","https://openalex.org/W4404511389","https://openalex.org/W4407273366","https://openalex.org/W6846589902","https://openalex.org/W6862893206"],"related_works":["https://openalex.org/W2367089784","https://openalex.org/W4281383848","https://openalex.org/W2344707987","https://openalex.org/W3021795417","https://openalex.org/W2791422888","https://openalex.org/W2949855111","https://openalex.org/W3006716706","https://openalex.org/W2991204057","https://openalex.org/W2617175248","https://openalex.org/W3036938294"],"abstract_inverted_index":{"Resolving":[0],"protein-ligand":[1,118],"interactions":[2],"in":[3,19,131,185],"atomic":[4],"detail":[5],"is":[6,37],"key":[7],"to":[8,83,144,162,168,182],"understanding":[9],"how":[10],"small":[11],"molecules":[12],"regulate":[13],"macromolecular":[14],"function.":[15],"Although":[16],"recent":[17],"breakthroughs":[18],"cryogenic":[20],"electron":[21],"microscopy":[22],"(cryo-EM)":[23],"have":[24,52],"enabled":[25],"high-quality":[26],"reconstruction":[27],"of":[28,34,66,115,127,150,188],"numerous":[29],"complex":[30],"biomolecules,":[31],"the":[32,63,132,163],"resolution":[33],"bound":[35],"ligands":[36,85],"often":[38],"relatively":[39],"poor.":[40],"Furthermore,":[41],"methods":[42],"for":[43,62,138,176],"building":[44,184],"and":[45,57,102,123,179],"refining":[46],"molecular":[47,154],"models":[48],"into":[49,86,153],"cryo-EM":[50,80,106,186],"maps":[51,187],"largely":[53],"focused":[54],"on":[55,112],"proteins":[56],"may":[58],"not":[59,142],"be":[60],"optimized":[61],"diverse":[64],"properties":[65],"small-molecule":[67],"ligands.":[68],"Here,":[69],"we":[70,108],"present":[71,130],"an":[72,104],"approach":[73,111],"that":[74],"integrates":[75],"artificial":[76],"intelligence":[77],"(AI)":[78],"with":[79],"density-guided":[81,180],"simulations":[82,156,181],"fit":[84],"experimental":[87,105,146],"maps.":[88],"Using":[89],"three":[90],"inputs:":[91],"1)":[92],"a":[93,99,113,173],"protein":[94],"amino":[95],"acid":[96],"sequence,":[97],"2)":[98],"ligand":[100,158],"specification,":[101],"3)":[103],"map,":[107],"validated":[109],"our":[110],"set":[114],"biomedically":[116],"relevant":[117],"complexes":[119],"including":[120],"kinases,":[121],"GPCRs,":[122],"solute":[124],"transporters,":[125],"none":[126],"which":[128,139],"were":[129],"AI":[133,140,178],"training":[134],"data.":[135],"In":[136],"cases":[137],"was":[141],"sufficient":[143],"predict":[145],"poses":[147],"outright,":[148],"integration":[149],"flexible":[151],"fitting":[152],"dynamics":[155],"improved":[157],"model-to-map":[159],"cross-correlation":[160],"relative":[161],"deposited":[164],"structure":[165],"from":[166],"40-71%":[167],"82-95%.":[169],"This":[170],"work":[171],"offers":[172],"straightforward":[174],"pipeline":[175],"integrating":[177],"model":[183],"ligand-protein":[189],"complexes.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2025-10-10T00:00:00"}
