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. 2017 Jul 16;(125):55640.
doi: 10.3791/55640.

Investigating Protein Sequence-structure-dynamics Relationships With Bio3D-web

Free PMC article

Investigating Protein Sequence-structure-dynamics Relationships With Bio3D-web

Shashank Jariwala et al. J Vis Exp. .
Free PMC article


We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) comparison of predicted internal dynamics via ensemble normal mode analysis. This integrated functionality provides a complete online workflow for investigating sequence-structure-dynamic relationships within protein families and superfamilies.

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    1. Kornev AP, Taylor SS. Dynamics-Driven Allostery in Protein Kinases. Trends Biochem. Sci. 2015;40(11):628–647. - PMC - PubMed
    1. Yao X-Q, Grant BJ. Domain-opening and dynamic coupling in the α-subunit of heterotrimeric G proteins. Biophys. J. 2013;105(2):L08–L10. - PMC - PubMed
    1. Henzler-Wildman KA, et al. Intrinsic motions along an enzymatic reaction trajectory. Nature. 2007;450(7171):838–844. - PubMed
    1. Boehr D, Nussinov R, Wright P. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 2009;5(11):789–796. - PMC - PubMed
    1. Teilum K, Olsen JG, Kragelund BB. Functional aspects of protein flexibility. Cell Mol Life Sci. 2009;66(14):2231–2247. - PubMed

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