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A large fraction of eukaryotic proteins contain unstructured tails or linkers. The presence of flexible regions allows these systems to experience a high level of mobility facilitating their biological function. The complex nature of protein rotation in such flexible modular systems precludes a straightforward application of hydrodynamic methods to calculate their rotational motional properties. We describe the workflow of HYdrodynamic CoUpling of Domains (HYCUD), a program for prediction of effective rotational correlation times in multidomain proteins. The usage of HYCUD is demonstrated by its application to the ribosomal protein L7/L12. Rotational correlation times predicted by HYCUD might be used to detect molecular switch events mediated by disorder-order transitions in interdomain linkers. The source code and documentation are available at www.mpibpc.mpg.de/106144/software. mzwecks@gwdg.de or nare@nmr.mpibpc.mpg.de Supplementary material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Citation

Nasrollah Rezaei-Ghaleh, Frederik Klama, Francesca Munari, Markus Zweckstetter. HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins. Bioinformatics (Oxford, England). 2015 Apr 15;31(8):1319-21

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PMID: 25505088

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