I am using hex as docking software, which assumes the ligand to be rigid. When I am trying the reverse, my protein as the receptor and the Cu2++ the final complex does not show any interaction, which should be.
The following two may help you:
FoldX:
http://www.pnas.org/content/102/29/10147.short
http://foldx.crg.es/
FINDSITE-metal:
http://onlinelibrary.wiley.com/doi/10.1002/prot.22913/full
http://cssb.biology.gatech.edu/findsite-metal
All the best,
Rob
PS in addition, and for in-depth studies at (metal) binding sites, think about Molecular Dynamics approaches instead of docking - you may find MD experts somewhere here
I am not sure if I got the question right. In case, you can reply to my comment.
My experience is based on docking, perhaps it may help. I guess the way docking code works is by performing a search in configuration space of the ligand (drug treated as rigid body), by that I mean rotations of the ligand in the enzymatic cavity. If I invert the process there might be different possible orientation taken by the enzyme in order to satisfy the same docking. This in practice may work but it could be very tedious and time consuming.
Thanks Adolfo for the kind input.
There are certain copper attaching signatures in the protein I am dealing with. I am trying to find whether ionic copper (the form which Cu takes in solution), attaches to those signatures OR to any other places. For my case I think the orientation is not that important.
I would love have your comment in return.
I don't think Hex (or any standard docking software) is the right choice for a problem such as this. They're primarily based upon geometric fit, which becomes pretty much irrelevant when your ligand is a single spherical ion. Affinity between copper and any site of your protein will be based upon charge, van der Waals interactions, and geometric agreement with preferred coordination arrangements. The latter in particular are not handled in any docking software I'm aware of (except FlexX, but only where the ion is a part of the docking site for your ligand) - or, for that matter, in any classical molecular dynamics forcefields. There's no simple approach, I think.
Both of your answers does not point to a rosy picture for me. Thanks a ton for your inputs.
The following two may help you:
FoldX:
http://www.pnas.org/content/102/29/10147.short
http://foldx.crg.es/
FINDSITE-metal:
http://onlinelibrary.wiley.com/doi/10.1002/prot.22913/full
http://cssb.biology.gatech.edu/findsite-metal
All the best,
Rob
PS in addition, and for in-depth studies at (metal) binding sites, think about Molecular Dynamics approaches instead of docking - you may find MD experts somewhere here
Hello Robert Rentzsch,
Thanks for the valuable input. FoldX is perfect. I will also follow the MD approach suggested by you. Could you by any chance suggest some literatures related to MD approach ?
Hi Pratim,
Sorry, but I would have to search just as you would. So you may want to a) create a new question specifically regarding MD of metal ions with proteins AND/OR b) start searching the web (Google, Google Scholar, PubMed, ...). I would probably start with option b and search for st like "metal ion protein binding molecular dynamics" initially. Be creative.
Good luck!
Rob
Oh my bad !! Thanks for keyword suggestions though and for the "be creative" wish too !!
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