ArticlebioRxiv : the preprint server for biology2025
Validation of helical symmetry parameters in EMDB.
Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Helical symmetry is a structural feature of many biological assemblies, including cytoskeletons, viruses, and pathological amyloid fibrils. One unique metadata for helical structures is the helical parameters, twist and rise. With the increasing number of helical structures being resolved through cryo-EM and deposited in the EMDB, there is a growing possibility of errors in the metadata associated with these entries. During our cryo-EM analysis of protein amyloids and the development of helical analysis tools, we realized that many deposited helical parameters appear inconsistent with the associated density maps. Herein, we have developed a comprehensive validation process that examines the consistency of these parameters by combining high-throughput computational evaluation with manual verification. Multiple errors were identified and corrected for ~14% of the total entries, including missing parameters, swapped twist and rise values, incorrect sign of twist angles, partial symmetries, and bona fide errors. Our validation code, workflow, and the validated parameters are publicly available.
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