EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

By B. Barad, Nathaniel Echols, R. Wang, Yifan Cheng, Frank DiMaio, Paul D. Adams, James S. Fraser. 2015

699 citations recorded by the source corpus.

Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EMRinger, a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

Subfields: Molecular Biology, Structural Biology, Surfaces, Coatings and Films

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, background): “The EMRinger (phenix.emringer) score quantifies how well the model backbone places side chains in density peaks that are consistent with rotameric conformations (Barad et al., 2015).”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, methodology): “The resulting model has much improved clashscore and EMRinger score (Barad et al., 2015) and no rotamer outliers, yet the number of Ramachandran plot outliers has increased compared to the original model (Table 1).”
Structure of the class D GPCR Ste2 dimer coupled to two G proteins (2020, positive): “Model validation was performed in PHENIX, Molprobity 53 and EMRinger 54 .”
Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology (2020, positive): “Models were reﬁned and relaxed using Rosetta using both sharpened and unsharpened maps (Frenz et al., 2019; Wang et al., 2016) and validated using Molprobity (Chen et al., 2010), Phenix (Liebschner et al., 2019), Privateer (Agirre et al., 2015) and EMRinger (Barad et al., 2015).”
The human coronavirus HCoV-229E S-protein structure and receptor binding (2019, methodology): “The atomic model was validated using Molprobity (Williams et al., 2018) , EMRinger (Barad et al., 2015) and the comprehensive validation (cryo-EM) tool in Phenix (Afonine et al., 2018b) .”
Cryo-EM targets in CASP13: overview and evaluation of results (2019, methodology): “For assessing the goodness-of-fit, we used three software packages: PHENIX,19 TEMPy,20,21 and EMRinger.22 The overall model-tomap goodness-of-fit is quantified using PHENIX's real space correlation coefficients—CCvolume, CCmask, and CCpeaks,—each probing different aspects of model-to-map fit23; TEMP”
Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “215 The score is calculated by extracting the map densities around each dihedral angle, and searching for peaks in density values at 60 , 180 , and 300 , which are known to be favored positions for the C γ atom, based on high-resolution X-ray structures.”
New tools for the analysis and validation of cryo-EM maps and atomic models (2018, methodology): “Phenix tools and tools available through Phenix (Molprobity: Chen et al., 2010; EM-Ringer: Barad et al., 2015) were used to calculate various statistics such as Ramachandran plots, residue side-chain rotamer outliers, and model-map correlations.”
Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein (2020, neutral): “, 2010), EMringer (Barad et al., 2015), Phenix (Liebschner et al.”