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.

Papers:

• "Predicting the Rotational Tumbling of Dynamic Multidomain Proteins and Supramolecular Complexes"  Rezaei-Ghaleh, Nasrollah; Klama, Frederik; Munari, Francesca; Zweckstetter, Markus;  ANGEWANDTE CHEMIE-INTERNATIONAL EDITION  Oct 2013 Vol: 52(43) p11410-11414
• "Long-Range Correlated Dynamics in Intrinsically Disordered Proteins"  Parigi, Giacomo; Rezaei-Ghaleh, Nasrollah; Giachetti, Andrea; Becker, Stefan; Fernandez, Claudio; Blackledge, Martin; Griesinger, Christian; Zweckstetter, Markus; Luchinat, Claudio;  JOURNAL OF THE AMERICAN CHEMICAL SOCIETY  2014 DOI: 10.1021/ja506820r

Contact: mzwecks@gwdg.de

Download

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

Dependencies

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

Setup

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 = ".".