I am trying to dock a predicted antibody structure onto an epitope. I don't know the exact epitope, but I know some key residues and I've been using a shape complementarity server to give me a starting point before running the local docking2 protocol. I'm not getting a great "funnel" of my result files, but more importantly when I look at my structures in PyMOL there doesn't seem to be any contacting surface area between my 2 proteins- it looks OK by eye, but all of the residues are greater than 1.4 angstroms apart. How does ROSIE define "contact" in the docking protocol when it is refining the side chains?
has a chart giving covalent bond lengths up to 154 pm = 1.54 Angstroms for organic compounds.
says "in the X−H…Y system, where the dots represent the hydrogen bond:
the X−H distance is typically ≈110 pm, whereas the H…Y distance is ≈160 to 200 pm."
says "the disulfide bond is about 2.05 Å in length, about 0.5 Å longer than a C–C bond."
says "the distance between the residues participating in the salt bridge is also cited as being important.
The distance required is less than 4 Å (400 pm). Amino acids greater than this distance do not qualify
as forming a salt bridge."
Does that help?
Thanks AdoCbl, I think I was being a little too stringent with my cutoff.
I am a new user of the rosettacommons forum. Will you please tell me how to submit a new post? I cannot find the corressponding button.
To submit a new post, click on "New topic" below "Home >> Forums >> ROSIE"
and above "Topic / Topic starter" (see the image file attached below). This takes
you to the page: https://www.rosettacommons.org/node/add/forum/99
I hope this helps,