I synthesis new ligand ,that ligand react with divalent metals it form metal complex.l used maestro 9.0 for docking the protein with ligand but the problem was maestro 9.0 (not only that all the docking software) not accepted the coordination bond between the metal and ligand in the .mol or .sdf format.so how to dock metal complex with protein.
firstly u tell me which biomolecule considered as drug target? Is it proteins involved in cancer? for the docking of your metal containing ligands, u can use Hyperchem 2015 and Tclpro1.2. idock is the best tool for docking of ligand-metal complex.
Hi you can convert the molecule in maestro as .mae and after that maestro surely recognizes the potential metal coordination. Alternatively you can run protein preparation wizard using the complex generated by docking and the metal coordination bonds will appear in your complex
molecular docking visualization tool -chimera 1.10 (freeware)
Accelrys molecular viewer (demo/commercial)
Mostly I hear this problem in docking, it is necessary to track bond distance when you using every software, for example for maestro we normally for zero-bond for metal and ligand instead of coordination. but if you want to see your ligand have the ability to bind to the metal in protein, track the Bond distance (like Zn-n around 2-2.2A). simulation and docking forcefield couldn't recognize the metal coordination, but if there is it is possible to recognize it by distance
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