Some complexes are buried or shredded

[Tsuchihashi-ryo]

Thank you for your work and for opening it up.

In some protein complexes, chains are colliding, buried, or entangled with each other.
In addition, sometimes the residues in the chains are separated from each other and shredded.
Can these be prevented by providing constraints?
In my experiment, more than 70% of the complexes were within 2 Å of each other (probably bumping into each other) of residues in different chains.
This may be because I am dealing with proteins that are too large (600~1000 residues in total), but I would like to know if this is possible to solve.

complex.zip

[yuemhu]

Hi, I also encountered the same problem as you. I guess GeoDock may discard the branch chain information. I was wondering if you solved this problem?