CryoFlex characterizes structural motion between conformations directly from cryo-EM density maps
- 1Beijing Institute of Technology
Abstract
Heterogeneous cryo-EM reconstruction methods can resolve multiple conformational states, but understanding their functional implications often requires determining which regions move between states and quantifying their displacement magnitudes. Comparing atomic models can quantify motion, but flexible regions are often incompletely modeled. Direct map comparison is limited by variable map quality and ambiguous correspondence between displaced density features. Here, we present CryoFlex, a method that estimates the direction and magnitude of structural motion directly from reconstructed density maps of selected states. The resulting motion analysis supports functional interpretation and guides downstream structure processing. CryoFlex localized and quantified structural motion across diverse map pairs, including those with incomplete atomic-model coverage or weak local density. Against C; displacements, CryoFlex achieved an endpoint error of about 1 angstrom. In separate benchmarks, it outperformed registration baselines on clean and noisy inputs. Thus, CryoFlex complements heterogeneous reconstruction workflows with direct quantification of structural motion between reconstructed states.
Related
- Designed nanofiber immunogens prime antibody responsesto diverse conformations of the HIV-1 fusion peptide
- ConforFlux: Particle-Guided Trunk Repulsion for Diverse Protein Conformations
- Structural identifiability of partially-observed stochastic processes: from single-particle trajectories to total particle density data
- Dynamic endothelial ephrin-B2 and EphB4 expression characterizes hyaloid vessel regression
- Functional guild analysis characterizes gut microbiome responses to heat stress in thermotolerant and thermosensitive lactating sows across three omics layers
BibTeX
@misc{dong2026cryoflex,
title = {{CryoFlex characterizes structural motion between conformations directly from cryo-EM density maps}},
author = {H. Dong and F. Li and Y. Chen and S. Tang and C. Ji and X. Wang and Z. Lu and B. Hu and F. Zhang and X. Wan},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.01.748519},
url = {https://www.biorxiv.org/content/10.64898/2026.09.01.748519v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - CryoFlex characterizes structural motion between conformations directly from cryo-EM density maps
AU - H. Dong
AU - F. Li
AU - Y. Chen
AU - S. Tang
AU - C. Ji
AU - X. Wang
AU - Z. Lu
AU - B. Hu
AU - F. Zhang
AU - X. Wan
PY - 2026
DA - 2026/09/01
PB - bioRxiv
DO - 10.64898/2026.09.01.748519
UR - https://www.biorxiv.org/content/10.64898/2026.09.01.748519v1
AB - Heterogeneous cryo-EM reconstruction methods can resolve multiple conformational states, but understanding their functional implications often requires determining which regions move between states and quantifying their displacement magnitudes. Comparing atomic models can quantify motion, but flexible regions are often incompletely modeled. Direct map comparison is limited by variable map quality and ambiguous correspondence between displaced density features. Here, we present CryoFlex, a method that estimates the direction and magnitude of structural motion directly from reconstructed density maps of selected states. The resulting motion analysis supports functional interpretation and guides downstream structure processing. CryoFlex localized and quantified structural motion across diverse map pairs, including those with incomplete atomic-model coverage or weak local density. Against C; displacements, CryoFlex achieved an endpoint error of about 1 angstrom. In separate benchmarks, it outperformed registration baselines on clean and noisy inputs. Thus, CryoFlex complements heterogeneous reconstruction workflows with direct quantification of structural motion between reconstructed states.
ER -