ArticleFrontiers in molecular biosciences2021
Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution.
Article in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations.Communications chemistry · 2025Article
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
- Automated simulation-based membrane protein refinement into cryo-EM data.Biophysical journal · 2023Article
- Automated Protein Secondary Structure Assignment from CBiomolecules · 2022Article
- Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity.Biomolecules · 2022Review
- Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation.Biochemical Society transactions · 2021Review
- Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies.Molecules (Basel, Switzerland) · 2021Article
- Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.Journal of chemical information and modeling · 2021Article
- Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II FromFrontiers in molecular biosciences · 2021Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Structure determination using cryo-electron microscopy (cryo-EM) medium-resolution density maps is often facilitated by flexible fitting. Avoiding overfitting, adjusting force constants driving the structure to the density map, and emulating complex conformational transitions are major concerns in the fitting. To address them, we develop a new method based on a three-step multi-scale protocol. First, flexible fitting molecular dynamics (MD) simulations with coarse-grained structure-based force field and replica-exchange scheme between different force constants replicas are performed. Second, fitted Cα atom positions guide the all-atom structure in targeted MD. Finally, the all-atom flexible fitting refinement in implicit solvent adjusts the positions of the side chains in the density map. Final models obtained via the multi-scale protocol are significantly better resolved and more reliable in comparison with long all-atom flexible fitting simulations. The protocol is useful for multi-domain systems with intricate structural transitions as it preserves the secondary structure of single domains.
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