Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.
Catherine L LawsonAndriy KryshtafovychGrigore D PintilieStephen K BurleyJiri CernyVincent B ChenPaul EmsleyAlberto GobbiAndrzej JoachimiakSigrid NorengMichael G PrisantRandy J ReadJane S RichardsonAlexis L RohouBohdan SchneiderBenjamin D SellersChenghua ShaoElizabeth SourialChris I WilliamsChristopher J WilliamsYing YangVenkat AbbarajuPavel V AfonineMatthew L BakerPaul S BondThomas L BlundellTom BurnleyArthur CampbellRenzhi CaoJianlin ChengGrzegorz ChojnowskiKathryn D CowtanFrank DimaioReza EsmaeeliNabin GiriHelmut GrubmüllerSoon Wen HohJie HouCorey F HrycCarola HunteMaxim IgaevAgnel-Praveen JosephWei-Chun KaoDaisuke KiharaDilip KumarLijun LangSean LinSai Raghavendra Maddhuri Venkata SubramaniyaSumit MittalArup MondalNigel W MoriartyAndrew MuenksGarib N MurshudovRobert A NichollsMateusz OlekColin M PalmerAlberto PerezEmmi PohjolainenKarunakar R PothulaChristopher N RowleyDaipayan SarkarLuisa U SchäferChristopher J SchlicksupGunnar F SchröderMrinal ShekharDong SiAbhishek SingharoyOleg V SobolevGenki TerashiAndrea C VaianaSundeep C VedithiJacob VerburgtXiao WangRangana WarshamanageMartyn David WinnSimone WeyandKeitaro YamashitaMinglei ZhaoMichael F SchmidHelen M BermanWah ChiuPublished in: Nature methods (2024)
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 contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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