Hi Tommi
Yes, AMPLE does well with coiled-coils. The QUARK route is the easiest
to try. In your position I would simply trim a bit of sequence off
either end. Maybe you can see homologs that are a bit shorter at one
terminus? In any case, that's unlikely to affect the modelling and we've
seen QUARK make good models of coiled-coil proteins.
For Rosetta modelling we simply recommend you use the Robetta server
http://robetta.bakerlab.org/fragmentsubmit.jsp for fragment libraries.
Unless you're processing large numbers of sequences it's not worth
getting to grips with local fragment library generation. At the moment
CCP4online takes a file of ready-made models, not carrying out the
actual modelling for you. Doing local Rosetta modelling via AMPLE is as
described here
https://ample.readthedocs.io/en/latest/examples/rst/abinitio.html#example-abinitio
Recently, in collaboration with Owen Davies in Newcastle, we've made
some big improvements to AMPLE's abilities with coiled-coils, involving
more bespoke modelling protocols, both of a single chain and, where the
information is known, of a parallel oligomer. I gather Owen has been in
touch with you about these. The code is available but is not in the
current CCP4 distribution. We're also planning to improve the AMPLE
documentation in the next few months and we'll include an example of use
of this new coiled-coil mode at that time.
Best wishes
Dan
On 07/10/2019 22:33, Kajander, Tommi A wrote:
Hello,
We have a bit tricky case of coiled coil protein with good data (2.05Å) for
dimeric coiled coil (dimer in AU) - looks like AMPLE might be a way
to solve such cases, if you know other good programs please suggest (Better yet
if there is a clear how-to manual)
Some technical tips on usage for generation of fragments for AMPLE would be of
help, not completely on top of that… (running the QUARK server, the real
sequence is bit over 200 aa so not sure what is the best approach here?
Rosetta? any how-to for that.. well i am running Robetta fragments too).
with AMPLE can I do this with the online server or better run locally (need
Rosetta installed I take it?)
Suppose I could try Rosetta-MR also, but to my recollection that requires some
kind of a phaser hit first to be improved, and i dont think I am there.
Thanks for any comments,
Best,
Tommi
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Prof Daniel Rigden
Institute of Integrative Biology
Room 101, Biosciences Building
University of Liverpool
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