On Fri, Feb 20, 2015, Urszula Uciechowska wrote:
> I would like to also try the constraints in sander to fold the ssDNA.
> Which constraints should be the best for this case? I have attached the 2D
> ssDNA conformation that I would like to get.
It looks like you are trying to solve the RNA/DNA folding problem (going from
secondary structure to a three-dimensional model.) This is an unsolved
problem in general. The pseudoknot example in NAB gives lots of information
about how to specify the base pairs that you want. But this provides no
guarantee that the rest of the conformation will make sense.
Bottom line: be aware that this is a real research problem, and not just a
matter of finding the right program or the correct input variables. This is
turn means that you have to think about what you want to do with the result:
in some cases, a very rough answer might be all one needs; in other cases,
not.
....dac
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Received on Fri Feb 20 2015 - 09:00:02 PST
