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Khanh Dao Duc on Muck Rack

Khanh Dao Duc

As seen in: Frontiers, BioRxiv, Cell Press, medRxiv
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Articles

Advanced coarse-grained model for fast simulation of nascent polypeptide chain dynamics within the ribosome

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By Ella Teasell, Simcha Srebnik, Khanh Dao Duc
| buff.ly
Get full text access Log in, subscribe or purchase for full access. References 1. Rodnina, M.V. ∙ Beringer, M. ∙ Wintermeyer, W. How ribosomes make peptide bonds Trends Biochem. Sci. 2007; 32:20-26 2. Thommen, M. ∙ Holtkamp, W. ∙ Rodnina, M.V. Co-translational protein folding: progress and methods Curr. Opin. Struct. Biol. 2017; 42:83-89 3. Lu, J. ∙ Kobertz, W.R. ∙ Deutsch, C. Mapping the electrostatic potential within the ribosomal exit tunnel J. Mol. Biol. 2007; 371:1378-1391 4. Masse, M.M. ∙ Guzman-Luna, V. ...
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Detection of archaeal- and prokaryotic-like ribosome exit tunnels within eukaryotic kingdoms

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By Shiqi Yu, Simcha Srebnik, Khanh Dao Duc, Artem Kushner
| BioRxiv
Abstract The ribosome exit tunnel is a critical sub-compartment that actively regulates the folding and dynamics of nascent polypeptide chains during protein translation. In this study, we systematically examined tunnel structures of 762 ribosome models obtained through cryo-EM and X-ray crystallography, to quantify structural variations across different species and biological domains.
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A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-EM density maps

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By Chenwei Zhang, Anne Condon, Khanh Dao Duc
| BioRxiv
Abstract Advancements in deep learning (DL) have recently led to new methods for automated construction of atomic models of proteins, from single-particle cryogenic electron microscopy (cryo-EM) density maps. We conduct a comprehensive survey of these methods, distinguishing between direct model building approaches that only use density maps, and indirect ones that integrate sequence-to-structure predictions from AlphaFold.
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