I have one metallic-organic compound. I want to check its applications towards the clinical side. I am trying to find out interaction studies of my compound and the protein. Please suggest some good software which will give me idea for this, so I can proceed further.
Hi Ramesh, for docking of organometallic compound , first generate its correct 3D conformation. Also try to see that the metal is accepted during the docking simulation and correct charge is assigned on it. Rest procedure is same as in case of small molecule docking.
I am using Discovery Studio Client software for any docking I want to do.
You can simply use the PubChem database from the NCBI. It's free and it contains a lot of references and examples.
Try with http://bioinfo3d.cs.tau.ac.il/PatchDock/index.html
Hi vikash kumar, I need some clarity that i want to generate the 3d structure of my metallic drug or i have to generate the 3d structure of targeted molecule?
Thank you for all the answers i will carry out the experiment and if any doubts i will consult for further questions. thank you once again. see you later All the best
HI Ramesh , if you know the target protein(receptor) and if its structure( experimental or homology model) is available then only you can proceed with docking. In general first stage of docking involves , receptor preparation and ligand preparation. After that select the approprate docking software.
For example
Autodock (free)is for small molecules and even small peptides.
Glide is commercial ..... for small molecules
Dock6 (free)... for small molecules
FlexX(commercial)--for small molecules
SurflexX(commercial)-- for small molecules.
SwissDock(free)-- for small molecules.
You can try any of one or combinations.
For generartion of 3D structure of your ligand you can try Marvin sketch(free) or Chem Draw. You can also search Pubchem Database.
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