Hello everyone,
I have some homodimers generated via two different online docking servers z dock and cluspro. I performed molecular dynamics on the top 10 complexes from z dock and found two of them to be stable after MD. Now, I want to compare the complexes obtained from cluspro to these stable complexes on the basis of their orientation, so that I can save time on running MD for all the complexes from cluspro. If anyone can please tell me how can it be done.
I will be really grateful.
Thanks
You can do a more relax clustering so you get fewer structures. Another way to do it is to characterize the angular location and relative orientation of one monomer with respect to the other for each dimer. Look at http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b02403 and and the supplementary information of https://www.nature.com/articles/srep40109
You can superimpose the structures. This can be done via almost all of the modelling softwares. VMD, Chimera, PyMol, DS Studio etc.
Poses with structural rmsd lesser than 2.0 Ao is usually taken as acceptable.
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