A fully automatic method yielding initial models from high-resolution electron cryo-microscopy maps

By T. C. Terwilliger, Paul D. Adams, Pavel V. Afonine, O. Sobolev. 2018

124 citations recorded by the source corpus.

We report a fully automated procedure for the optimization and interpretation of reconstructions from cryo-electron microscopy (cryo-EM) data, available in Phenix as phenix.map_to_model. We applied our approach to 476 datasets with resolution of 4.5 Å or better, including reconstructions of 47 ribosomes and 32 other protein–RNA complexes. The median fraction of residues in the deposited structures reproduced automatically was 71% for reconstructions determined at resolutions of 3 Å or better and 47% for those at resolutions worse than 3 Å. A fully automated method for modeling protein and protein–RNA complex structure from cryo-EM data, requiring minimal user intervention, is described.

Subfields: Molecular Biology, Structural Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Structural Biology

Citations in the corpus

Real-space refinement in PHENIX for cryo-EM and crystallography (2018, methodology): “In two independent refinements, the first half map was taken either as deposited or modified with phenix.auto_sharpen (Terwilliger et al., 2018, submitted) to automatically optimally sharpen or blur the map.”
Advances in methods for atomic resolution macromolecular structure determination (2020, methodology): “…to reconstruct density maps with near-atomic resolution required the development of methods and software 76 that could be used to build and refine 77–79 molecular models from cryo-EM data, in some cases utilizing complex automated modeling 80,81 or molecular dynamics calculations 82–85 .”
Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies (2020, unknown): “Glycans weremodeled at possible N-linked glycosylation sites (PNGSs) in Coot using ‘blurred’ maps processed with a variety of B-factors (Terwilliger et al., 2018).”
Structural basis for loading and inhibition of a bacterial T6SS phospholipase effector by the VgrG spike (2020, unknown): “For Tle1, a partial initial model based on the primary sequence was built using phenix.map_to_model (Terwilliger et al , 2018a).”