Docking

I have performed a docking between a protein and a 15 residue peptide using flex pep dock. I have got a total score of around -1347, is this considered as good docking ? I am unable to predict whether the docking can be considered or not. Please help me. Thanks in advance:

The total score and other factors are as follows:

Hi,

I am trying to run on the Rosie server some docking2 tests with bound ligand in each protein. In fact, I would like to explore a situation of how two protein interacts with each other with bound ligand. However, when I launch jobs with ligand coordinates at its final site included in the PDB, the simulation fails and I receive an error message.

I, therefore, write to ask whether is it possible to do on ROSIE server?

I thank you all in advance,

Haresh

Hi,

I am trying to use protein-protein docking with unbound ligand protein and, I still get this error(see below ). I would appreciate any suggestion or solution.

Looking forward to hearing from you.

Haresh 

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I am docking an antibody that has 20 residues in the H3 loop.  I realize that this is a very challenging case.  From the 2017 paper by Weitzner and Gray, I understand the importance of a kink constraint in H3 loop modeling.  I want to know if the H3 loop remodeling that occurs during snugdock includes the kink constraint.  If not, I am concerned that the kink will be lost during remodeling, especially for this long loop.