HYdrodynamic CoUpling of Domains (HYCUD) is a Python-based program for prediction of rotational correlation time of folded protein domains in the context of flexible multidomain proteins and protein complexes with long disordered tails and/or interdomain linkers as well as intrinsically disordered proteins. HYCUD starts from a structural ensemble of the protein of interest together with a definition of its modular architecture, calculates the effective viscosity experienced locally by each of its modules and correspondingly scales the reorientational correlation time of isolated domains obtained through experiment or standard hydrodynamic calculations, and finally averages the scaled correlation times over the structural ensemble. The use of HYCUD has been validated in several protein systems differing in size, domain architecture, assembly state and disorder level.


Contact: mzwecks@gwdg.de


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 HYCUD Version   File   Size   MD5 
 v3.3.1   hycud-3.3.1.zip   36.12kB   e7573b465e3992ef80b59030deb247d0 
 hycud-3.3.1.tar.gz   22.28kB   45198717d9de25737963a0ad789f94b5 
 hycud-3.3.1.tzr.bz2   20.49kB   9854c7beb7b415c59903b3846d48fcf1 
 hycud-3.3.1.tzr.xz   19.73kB   41deb2720d4b83ec43e85d8d176f46cc 


Download Tutorial

 Type   File   Size   MD5 
 Tutorial Only   HYCUD_Tutorial.pdf   123.6kB   2a0c406444fdfddac34ec6ef6549a3d0 
 Tutorial with example files   hycud_tutorial.zip   55.49MB   5bd939e0d490ec829468aff0dde9e676 
 hycud_tutorial.tar.gz   55.62MB   374f3ef055349a07f6eb4a0bfe3796f4 
 hycud_tutorial.tar.bz2   35.40MB   9e834ea4b1f1c47318ada0e54f8c9b04 
 hycud_tutorial.tar.xz   9.878MB   e45221a382fba59dc8ea6929f801f0fc 



 Program   Recommended Version   Link 
 Python   ≥3.2   http://www.python.org 
 Perl   ≥5.0   http://www.perl.org 
 REMO     http://zhanglab.ccmb.med.umich.edu/REMO/ 
 HydroPro   10   http://leonardo.inf.um.es/macromol/programs/hydropro/hydropro.htm 



Unpack downloaded file. It will generate a directory called hycud-[version] which would be hycud-3.3.1 for version 3.3.1. In your home directory create a directory .hycud and copy the file Options.py from the hycud directory to this newly created directory. You may edit Options.ph in the directory .hycud to set where HYCUD can find REMO, and HydroPro, as well as where to put it'2s temporary files.

Please don't edit the file in the hycud directory, since HYCUD will update the options file in your home directory if new options are added with a newer version. Any changes in the Options.py file included with HYCUD will be overridden by the one in your home directory.

Change the line: default_calcHydr = "hydropro10-lnx.exe" to the path where the HydroPro executable can be found (only change the bold part). Once this is done, the --exe option does not need to be specified anymore.
Change the line: default_REMOdir = "/nmr5/nare/programs/REMO" to the directory where REMO can be found. Once this is done, the --REMOdir (or -R) option does not need to be specified anymore.
If you want HYCUD to put it's temporary files into a special directory you can edit the line default_temporaryStorage = ".".


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