AIMC Topic: Cryoelectron Microscopy
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DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction.
Nature methods
Dec 8, 2023
Three-dimensional structure modeling from maps is an indispensable step for studying proteins and their complexes with cryogenic electron microscopy. Although the resolution of determined cryogenic electron microscopy maps has generally improved, the...
Deep learning structural insights into heterotrimeric alternatively spliced P2X7 receptors.
Purinergic signalling
Nov 30, 2023
P2X7 receptors (P2X7Rs) are membrane-bound ATP-gated ion channels that are composed of three subunits. Different subunit structures may be expressed due to alternative splicing of the P2RX7 gene, altering the receptor's function when combined with th...
Classification of helical polymers with deep-learning language models.
Journal of structural biology
Nov 7, 2023
Many macromolecules in biological systems exist in the form of helical polymers. However, the inherent polymorphism and heterogeneity of samples complicate the reconstruction of helical polymers from cryo-EM images. Currently, available 2D classifica...
Genetically encoded multimeric tags for subcellular protein localization in cryo-EM.
Nature methods
Nov 6, 2023
Cryo-electron tomography (cryo-ET) allows for label-free high-resolution imaging of macromolecular assemblies in their native cellular context. However, the localization of macromolecules of interest in tomographic volumes can be challenging. Here we...
The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions.
Acta crystallographica. Section D, Structural biology
Nov 3, 2023
Model building and refinement, and the validation of their correctness, are very effective and reliable at local resolutions better than about 2.5 Å for both crystallography and cryo-EM. However, at local resolutions worse than 2.5 Å both the procedu...
Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics.
Molecules (Basel, Switzerland)
Oct 19, 2023
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interacti...
Artificial intelligence and the analysis of cryo-EM data provide structural insight into the molecular mechanisms underlying LN-lamininopathies.
Scientific reports
Oct 19, 2023
Laminins (Lm) are major components of basement membranes (BM), which polymerize to form a planar lattice on cell surface. Genetic alternations of Lm affect their oligomerization patterns and lead to failures in BM assembly manifesting in a group of h...
CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning.
Nature methods
Oct 2, 2023
DNA and RNA play fundamental roles in various cellular processes, where their three-dimensional structures provide information critical to understanding the molecular mechanisms of their functions. Although an increasing number of nucleic acid struct...
Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting.
Journal of chemical information and modeling
Sep 4, 2023
Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledg...
Biomolecular NMR in the AI-assisted structural biology era: Old tricks and new opportunities.
Biochimica et biophysica acta. Proteins and proteomics
Aug 11, 2023
Over the last 40 years nuclear magnetic resonance (NMR) spectroscopy has established itself as one of the most versatile techniques for the characterization of biomolecules, especially proteins. Given the molecular size limitations of NMR together wi...
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