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Integrating model simulation tools and cryo-electron microscopy
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DOI：10.1002/wcms.1642.png)
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Abstract
En 中文
The power of computer simulations, including machine-learning, has become an inseparable part of scientific analysis of biological data. This has significantly impacted the field of cryogenic electron microscopy (cryo-EM), which has grown dramatically since the resolution-revolution. Many maps are now solved at 3-4 angstrom or better resolution, although a significant proportion of maps deposited in the Electron Microscopy Data Bank are still at lower resolution, where the positions of atoms cannot be determined unambiguously. Additionally, cryo-EM maps are often characterized by a varying local resolution, partly due to conformational heterogeneity of the imaged molecule. To address such problems, many computational methods have been developed for cryo-EM map reconstruction and atomistic model building. Here, we review the development in algorithms and tools for building models in cryo-EM maps at different resolutions. We describe methods for model building, including rigid and flexible fitting of known models, model validation, small-molecule fitting, and model visualization. We provide examples of how these methods have been used to elucidate the structure and function of dynamic macromolecular machines.This article is categorized under:Structure and Mechanism > Molecular StructuresStructure and Mechanism > Computational Biochemistry and BiophysicsSoftware > Molecular Modeling
Keywords:
cryo-EM
model validation
molecular modeling
molecular simulations
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