Biology subjects

Sobolev, O. V.

Publications and source records attributed to Sobolev, O. V..

4 recordsLinked to original sources

bioRxiv2018

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

A recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 cryo-EM maps with resolutions of 4.5 [A] or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 cryo-EM model challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 [A] to 2.1 [A].

biophysics↗

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↗