I have been using Swissdock and BiosolveIT for molecular docking recently. However, I have an issue when I try to do the modelling for metal complexes (particularly Rhenium complexes). Both don't recognize the metal ion and I fail to upload my compound. Does any one know what will be the best way to model these rhenium complexes. I am willing to switch to another software if this will solve my problem.
Thanks
BiosolveIT (LeadIT), it can docked metalloenzyme, but in case of metal complex (ligand), it didn't.
You can use Molegro virtual docker software for docking of ligand-metal complex.
There are other also like Hyperchem, TclPro1.2, etc.
In general you need to have a good parametrization in any force field for the metal in question in order to obtain any reasonable results. This will be very hard for any transition metal, like Rhenium, as most transition metal ions can form complexes with multiple number of ligands and very different geometries.
There is no easy way to deal with it, particularly if you don't know the exact binding site. For docking I would try building a complex with a more usual metal and the same charge (e.g. replace Re2+ with Ca2+), though it's prone to false positives. If you have a potential bindign site the only rasonable methos is to switch to QM/MM to get an estimte of free energy binding.
Autodock may do that but if you can manually input your new metal coordinates into the force field parameter file
Mohammed Tarek, I was thinking the same, but I have no clue how to that. Do you have available any detailed description of how to do it?
Anu Manhas, Thanks for the reply. In case of using Molegro, any suggestions for preparing the ligand file so it can be recognized by the software as a metal complex
Please Dr. Review
http://autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4
http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock
- we could just edit the AD4_parameters.dat file with any text editor and add the following line at the end of our file
atom_par Re Rii epsii vol solpar -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
replacing variables with suitable values and
then save to the file....
Definitely, the best answer is from Bartosz Trzaskowski. You will need the parameters. If you don't have it, maybe you can calculate it using ab initio methods using for examples Gaussian software or use a metal with similar properties as a first approach. Otherwise, your results will not have chemical or biological sense.
atom_par Re 2.95 0.066 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques
October 2017Journal of Computational Chemistry
DOI: 10.1002/jcc.25080
I want calculate energies for enzyme without ligand in molegro virtual docking ??!
If any body is conversant for molecular docking of metal complexes I will be glad to know and collaborate
A.K. Goswami Article MetalDock: An Open Access Docking Tool for Easy and Reproduc...
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