i want to dock copper on my protein, which has metal binding site. can you please guide me step wise, how to perform this??
you can use Autodock tools. it's free and powerfull for protein-ligand docking.
which one. please provide me some web address. i choose previously hex dock. but i am not sure whether is docking is accurate or not. i want to get also the PDB file of copper. can u please guide me?
use the molecular converter web service convert to PDB file , in this online tool you can make many type of file formats
if you want to dock try it (http://mgltools.scripps.edu/) and link to get copper as ligand in here http://www.ncbi.nlm.nih.gov/pcsubstance/?term=Copper. i hope it can help u
u want only the copper atom or any compound with copper! anyways,try pubchem or chemspider to get the ligand. u might get the ligand in sdf format or so..convert it using molecule converters to pdb format. then try to dock with ur protein. i have used MVD,its good one. u can also use autodock or hex. all the best
i want to dock colon cancer causing proteins with my protein can you plz hlp me out
first u have to identify the metal binding site of ur protein i.e., the binding site residues.this u can do from pdb sum.then u have to generate suitable grid to those residues containing site.before grid generation u have to energy minimize ur protein as well as ur ligand i.e., copper.then u can dock ur copper to ur protein
@kompally Vani can u tell me how to generate grid and minimize the energy of structures? what all softwares are being used for this?
u can download maestro softwre free version through net...after downlading send me ur mail id il forward da instructn pdf file 2 u...by following it u can easily procced
hai vani thanks 4 ur information i too wanna dock with some cancer compounds can you please tell me which software can i use ..... and it should be accepeted for paper ...
U can use molegro virtual docker soft ware for help u try to download video tutorial and go for yor need
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