biostudies-literatureLawson CLU.S. Department of Energy (DOE)DST | Science and Engineering Research Board (SERB)U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)Deutsche Forschungsgemeinschaft (German Research Foundation)Medical Research CouncilNational Science Foundation (NSF)Wellcome TrustNIGMS NIH HHSBiotechnology and Biological Sciences Research Council1340-1348https://www.ebi.ac.uk/biostudies/studies/S-EPMC11526832biostudies-literatureUnknown21(7)The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contacNature methodsOutcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.PMC11526832MC_UP_A025_1012R01 GM146340CRG/2022/002761R01 GM093123R01 GM133840208398/Z/17/ZR01GM133198RTG 2756BB/S007083/1R35 GM143052R01GM073919CIBSS - EXC-2189 - 390939984R01GM071939R24GM141254R24 GM141254R35GM131883BB/T012935/1R01 GM123089R01 GM079429BB/S005099/1R01 GM157729DGE-1762114IIS2211598DESC0019749DBI-1832184R01GM133840209407/Z/17/ZR01 GM133198R01GM123089R01GM146340DE-AC02-05CH11231DE-AC02-06CH11357R01 GM073919P01 GM063210R01 GM071939P01GM063210R35 GM131883MR/V000403/1R01GM079429CHE-2235785Lang LRowley CNGiri NSchlicksup CJLin SVedithi SCTerashi GWilliams CJSourial EWilliams CIPohjolainen ELawson CLSchafer LUEmsley PVaiana ACKao WCSchroder GFWang XHunte COlek MBaker MLMurshudov GNMaddhuri Venkata Subramaniya SRPintilie GDSchmid MFBurnley TNicholls RAEsmaeeli RBlundell TLBerman HMPalmer CMYang YNoreng SSi DWeyand SSobolev OVPrisant MGVerburgt JKryshtafovych AWarshamanage RJoachimiak AChojnowski GPothula KRAfonine PVJoseph APDiMaio FShao CMoriarty NWHryc CFBurley SKPerez AZhao MGobbi ASchneider BChiu WSingharoy ACheng JKihara DBond PSSarkar DChen VBRichardson JSRohou ALAbbaraju VSellers BDHoh SWWinn MDCowtan KDCerny JGrubmuller HKumar DIgaev MMittal SHou JMondal AShekhar MMuenks ACampbell AYamashita KCao RRead RJfalseOutcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contac2024-01-01T00:00:00Z2024 Jul2026-06-02T12:10:33.046Z2026-04-18T03:11:18.945ZS-EPMC115268323891860410.1038/s41592-024-02321-7