HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins

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Motivation: 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.

Availability and implementation: The source code and documentation are available at www.mpibpc.mpg.de/106144/software.

Contact:mzwecks@gwdg.de or nare@nmr.mpibpc.mpg.de

Supplementary information: Supplementary material is available at Bioinformatics online.

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