This seems like a good problem for SAXS rigid body modeling. We previously used an approach based on docking models into SAXS envelopes with the constraint of 2-fold symmetry, followed by scoring the dimer models using the goodness of fit to the experimental curve (1). Another approach would be to use CORAL, which we have used to model a multi domain monomer (2). CORAL allows the enforcement of symmetry for oligomers. Either way, you can use target decoy analysis to get an idea of the confidence in the models (2). In your case knowing the quaternary structure of the N-terminal domains provides a powerful constraint for SAXS modeling.
(1) http://www.ncbi.nlm.nih.gov/pubmed/22013066 (2) http://www.ncbi.nlm.nih.gov/pubmed/25137435 Jack Tanner Sent from Jack's iPad On May 12, 2015, at 12:56 AM, Victor Xiao <victor41...@gmail.com<mailto:victor41...@gmail.com>> wrote: Dear all, I am trying to model a full-length double-domain protein in dimer. The structure of both N and C terminal domains are known and the linker region of 5 residues are present in both structure (the linker might be flexible though). The N-terminal domain's structure is also a dimer, which can be used as another restraint. Does anyone know any good tool for modeling such full-length dimer? Thanks in advance. Best, Xiao
