@article{Lawson_C-2024_189977,
title = {Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge},
author = {Lawson, C. and Kryshtafovych, A. and Pintilie, G. and Burley, S. and Černý, J. and Chen, V. and Emsley, P. and Gobbi, A. and Joachimiak, A. and Noreng, S. and Prisant, M. and Read, R. and Richardson, J. and Rohou, A. and Schneider, B. and Sellers, B. and Shao, C. and Sourial, E. and Williams, C. and Williams, C. and Yang, Y. and Abbaraju, V. and Afonine, P. and Baker, M. and Bond, P. and Blundell, T. and Burnley, T. and Campbell, A. and Cao, R. and Cheng, J. and Chojnowski, G. and Cowtan, K. and DiMaio, F. and Esmaeeli, R. and Giri, N. and Grubmüller, H. and Hoh, S. and Hou, J. and Hryc, C. and Hunte, C. and Igaev, M. and Joseph, A. and Kao, W. and Kihara, D. and Kumar, D. and Lang, L. and Lin, S. and Maddhuri Venkata Subramaniya, S. and Mittal, S. and Mondal, A. and Moriarty, N. and Muenks, A. and Murshudov, G. and Nicholls, R. and Olek, M. and Palmer, C. and Oteo Perez, A. and Pohjolainen, E. and Pothula, K. and Rowley, C. and Sarkar, D. and Schäfer, L. and Schlicksup, C. and Schröder, G. and Shekhar, M. and Si, D. and Singharoy, A. and Sobolev, O. and Terashi, G. and Vaiana, A. and Vedithi, S. and Verburgt, J. and Wang, X. and Warshamanage, R. and Winn, M. and Weyand, S. and Yamashita, K. and Zhao, M. and Schmid, M. and Berman, H. and Chiu, W.},
month = {jun},
year = {2024},
abstract = {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.},
pages = {1340-1348},
volume = {21},
journal = {Nature Methods},
publisher = {Springer Nature},
url = {https://doi.org/10.1038/s41592-024-02321-7},
}
