EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

• Published in: Nature methods Vol. 12; no. 10; pp. 943 - 946
• Main Authors: Barad, Benjamin A, Echols, Nathaniel, Wang, Ray Yu-Ruei, Cheng, Yifan, DiMaio, Frank, Adams, Paul D, Fraser, James S
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.10.2015; Nature Publishing Group
• Subjects: 101/28; 631/114/2415; 631/114/794; 631/1647/2258/1258/1259; 631/45/612; Amino acids; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical Engineering/Biotechnology; brief-communication; Cryoelectron Microscopy - methods; Cryogenic engineering; Crystallography, X-Ray; Databases, Protein; Electron microscopes; Electron microscopy; Image Processing, Computer-Assisted - methods; Innovations; Life Sciences; Microscopy; Models, Molecular; Molecular structure; Observations; OTHER INSTRUMENTATION; Protein Conformation; Proteins - chemistry; Proteomics; Reproducibility of Results; Software; TRPV Cation Channels - chemistry
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/nmeth.3541

The fit of atomic models of protein structures to high-resolution cryo-electron microscopy maps can be assessed with a validation tool, EMRinger. 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.