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This repository contains the results of a hierarchical atomic resolution perception (HARP) calculation on each of the cryoEM structures deposited in the Protein Data Bank (PDB) prior to January 1, 2023. Top-level group names are the PDB IDs of the structures. HDF5 group attributes for each entry are certain metadata extracted from the mmCIF files associated with each entry. HDF5 datasets within each group are indexed relative to each other (i.e., are of the same length).
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Scale-dependent hierarchical resolution: applications to atomic resolution and model validation in cryoEM
The recent cryoEM resolution revolution has had a tremendous impact on our ability to investigate biomolecular structure and function. However, outstanding questions about the reliability of using a cryoEM-derived molecular model for interpreting experiments and building further hypotheses limit its full impact. Significant amounts of research have been focused on developing metrics to assess cryoEM model quality, yet no consensus exists. This is in part because the meaning of cryoEM model quality is not well defined. In this work, we formalize cryoEM model quality in terms of whether a cryoEM map is better described by a model with localized atomic coordinates or by a lower-resolution model that lacks atomic-level information. This approach emerges from a novel, quantitative definition of image resolution based upon the hierarchical structure of biomolecules, which enables computational selection of the length scale to which a biomolecule is resolved based upon the available evidence embedded in the experimental data. In the context of cryoEM, we develop a machine learning-based implementation of this framework, called hierarchical atomic resolution perception (HARP), for assessing local atomic resolution in a cryoEM map and thus evaluating cryoEM model quality in a theoretically and statistically well-defined manner. Finally, using HARP, we perform a meta-analysis of the cryoEM-derived structures in the Protein Data Bank (PDB) to assess the state of atomic resolution in the field and quantify factors that affect it.
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- Award ID(s):
- 2137630
- PAR ID:
- 10560635
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Institution:
- bioRxiv
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Posted Content:
- https://doi.org/10.1101/2023.10.17.562748
