ligand dock residue selection

[Anonymous]

Is it posible to select specific residues (both sidechains and backbone) which will be modified during the procedure, leaving the rest of the protein structure unchanged? I’m thinking on something like the res file for the other applications.

Thanks in advance.

[Anonymous]

As far as sidechains go, the resfile is respected by most applications. I’ve never tried ligand docking but I’d be surprised if it did not respect the resfile. Let me know what you find.

As far as backbone torsional degrees of freedom…that’s a tougher problem. Loop modeling lets you choose your loops, other than that protocols typically choose freedoms internally.

[Anonymous]

to the best of my knowledge, the ligand dock protocol doesn’t actually respect resfiles. instead, every time a packing step happens in the protocol, the residues surrounding the current ligand position will be selected for repacking (and backbone/chi minimization ). the distance cutoff used to determine whether a residue is part of the interface is the neighbor radius of the residue in question (as specified in the .params files ) plus 6 angstroms.

cheers,
Florian Richter
PhD student, Baker group

> Is it posible to select specific residues (both sidechains and backbone) which will be modified during the procedure, leaving the rest of the protein structure unchanged? I’m thinking on something like the res file for the other applications.
>
> Thanks in advance.
>

[Author]

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