CCCP 
 CCCP (Coiled-coil Crick Parameterization)
This program generates coiled-coil structures based on specified Crick parameters[1-2]. Multiple structures can be generated that span a range of parameters. Contact gevorg.grigoryan at gmail dot com with bug reports and requests.


Number of chains:

Chain length:

Coiled-coil parameters

Parameter (symbol, unit) Star End # Samples
Rise per residue (d, Å): constrain*
Superhelical radius (Ro, Å): adjust** vary
together
Superhelical frequency (ωo, °/aa):
(negative means left-handed superhelix)		 adjust**
Pitch angle (α, °): adjust**
α-helical radius (R1, Å):
α-helical frequency (ω1, °/aa):
Symmetry (limits variable parameters):
     Cn
     Dn
     Do not impose symmetry
Forcefield minimize final backbone (CA atoms held fixed)
Create a poly-alanine backbone, not a poly-glycine

Chain-wise parameters

Parameter (symbol, unit) Star End Steps
Specify one value for each chain after the first. Separate values with spaces, commas or semicolons. Note that by default, individual chain parameters are traversed independently.
α-helical phase (φ1, °):
Superhelical phase offset (Δφ0, °):
Z offset (Zaa', Å):
Orientation versus first chain (p – parallel, ap – antiparallel):
Couple chain variations

Resulting number of structures (not to exceed 1,000):


* – Constrain coiled-coil parameters to be consistent with the specified value (or range of values) of rise per residue.
** – Use the corresponding parameter as the adjastable to ensure that the rise per residue is at its set value.

[1] F. H. Crick, "The Fourier Transform of a Coiled Coil", Acta Cryst., 6: 685 (1953)
[2] G. Grigoryan, W. F. DeGrado, "Probing Designability via a Generalized Model of Helical Bundle Geometry", J. Mol. Biol., 405(4): 1079-1100 (2011)