Journal Article

FZJ-2024-06373

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

Lawson, C. L. ; Kryshtafovych, A. ; Pintilie, G. D. ; Burley, S. K. ; Černý, J. ; Chen, V. B. ; Emsley, P. ; Gobbi, A. ; Joachimiak, A. ; Noreng, S. ; Prisant, M. G. ; Read, R. J. ; Richardson, J. S. ; Rohou, A. L. ; Schneider, B. ; Sellers, B. D. ; Shao, C. ; Sourial, E. ; Williams, C. I. ; Williams, C. J. ; Yang, Y. ; Abbaraju, V. ; Afonine, P. V. ; Baker, M. L. ; Bond, P. S. ; Blundell, T. L. ; Burnley, T. ; Campbell, A. ; Cao, R. ; Cheng, J. ; Chojnowski, G. ; Cowtan, K. D. ; DiMaio, F. ; Esmaeeli, R. ; Giri, N. ; Grubmüller, H. ; Hoh, S. W. ; Hou, J. ; Hryc, C. F. ; Hunte, C. ; Igaev, M. ; Joseph, A. P. ; Kao, W.-C. ; Kihara, D. ; Kumar, D. ; Lang, L. ; Lin, S. ; Maddhuri Venkata Subramaniya, S. R. ; Mittal, S. ; Mondal, A. ; Moriarty, N. W. ; Muenks, A. ; Murshudov, G. N. ; Nicholls, R. A. ; Olek, M. ; Palmer, C. M. ; Perez, A. ; Pohjolainen, E. ; Pothula, K. R. ; Rowley, C. N. ; Sarkar, D. ; Schäfer, L. U. ; Schlicksup, C. J. ; Schröder, G. F.FZJ* ; Shekhar, M. ; Si, D. ; Singharoy, A. ; Sobolev, O. V. ; Terashi, G. ; Vaiana, A. C. ; Vedithi, S. C. ; Verburgt, J. ; Wang, X.FZJ* ; Warshamanage, R. ; Winn, M. D. ; Weyand, S. ; Yamashita, K. ; Zhao, M. ; Schmid, M. F. ; Berman, H. M. ; Chiu, W.

2024
Nature Publishing Group London [u.a.]

This record in other databases:      

Please use a persistent id in citations: doi:10.1038/s41592-024-02321-7  doi:10.34734/FZJ-2024-06373

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.

---

Contributing Institute(s):

1. Strukturbiochemie (IBI-7)

Research Program(s):

1. 5241 - Molecular Information Processing in Cellular Systems (POF4-524) (POF4-524)

Appears in the scientific report 2024

---

Database coverage:
; ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; DEAL Nature ; Ebsco Academic Search ; Essential Science Indicators ; IF >= 40 ; JCR ; Nationallizenz ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

---