Biology subjects

Afonine, P. V.

Publications and source records attributed to Afonine, P. V..

4 recordsLinked to original sources

bioRxiv2018

New tools for the analysis and validation of Cryo-EM maps and atomic models

Recent advances in the field of electron cryo-microscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of bio-macromolecules solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically for cryo-EM validation are required. We discuss new computational methods and tools implemented in Phenix, including d99 to estimate resolution, phenix.auto_sharpen to improve maps, and phenix.mtriage to analyze cryo-EM maps. We suggest that cryo-EM half-maps and masks are deposited to facilitate evaluation and validation of cryo-EM derived atomic models and maps. We also present the application of these tools to deposited cryo-EM atomic models and maps.

bioinformatics↗

bioRxiv2018

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

A fully automated procedure for optimization and interpretation of reconstructions from cryo-EM is developed and applied to 476 datasets with resolution of 4.5 [A] 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 [A] or better and 47% for those at lower resolution.

biochemistry↗

bioRxiv2018

Real-space refinement in Phenix for cryo-EM and crystallography

This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data-restraints weight as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. Re-refinement of 385 cryo-EM derived models available in the PDB at resolutions of 6 [A] or better shows significant improvement of models and the fit of these models to the target maps.\n\nSynopsisA description of the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite and its application to re-refinement of cryo-EM derived models.

bioinformatics↗

bioRxiv2018

Automated map sharpening by maximization of detail and connectivity

SynopsisA procedure for optimizing the sharpening of a map based on maximizing the level of detail and connectivity of the map is developed and applied to 361 pairs of deposited cryo-EM maps and associated models.\n\nAbstractWe present an algorithm for automatic map sharpening that is based on optimization of detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high level of detail has a high surface area. The connectivity of the sharpened map is reflected in the number of connected regions defined by the same iso-contour surfaces, where a map with high connectivity has a small number of connected regions. By combining these two measures in a metric we term \"adjusted surface area\", we can evaluate map quality in an automated fashion. We use this metric to choose optimal map sharpening parameters without reference to a model or other interpretations of the map. Map sharpening by optimization of adjusted surface area can be carried out for a map as a whole or it can be carried out locally, yielding a locally-sharpened map. To evaluate the performance of various approaches, we use a simple metric based on map-model correlation that can reproduce visual choices of optimally-sharpened maps. The map-model correlation is calculated using a model with B-factors (atomic displacement factors, ADP) set to zero. We use this model-based metric to evaluate map sharpening, use it to evaluate map sharpening approaches and find that optimization of adjusted surface area can be an effective tool for map sharpening.

biochemistry↗