I understood that you want to ckeck with docking how your
ligands work in some proteins (inhibitor, substrate, inert). (It's not enogh.
You have to read about every protein to know them deeply). You should check the
Protein Data Bank (PDB) http://www.rcsb.org/pdb/home/home.do">http://www.rcsb.org/pdb/home/home.do to download X-ray
structures of different proteins and you can select a protein for docking taking
into acount the active part of the protein (reading publications about that
protein). But here I want to mention that in some cases the structure are not
complete for docking. For example the ammonia-lyase structures have tetramer
form, but in the PDB you can find them as dimer or two different dimer form.
From here, after you know the real
form of your protein and if this doesn't have the real form in the PDB you may
build the real form in SwissPDBViewer program http://spdbv.vital-it.ch/">http://spdbv.vital-it.ch/. It depends on
your ligands too how they will fit in the protein structure. You should
check the electrophilic or nucleophilic properties at the ligands and in the
active part (catalitic site) of the protein. For docking you
can use AutoDock http://autodock.scripps.edu/, FlexX http://www.biosolveit.de/flexx/ or
other programs. Hope this helps, Good
work, Amalia
From:
james peter jp07:+:sify.com <owner-chemistry[-]ccl.net> To: "Seff, Amalia Laura -id#3td-"
<slaurami[-]yahoo.com> Sent: Sunday, June 14, 2009 3:14:11 PM Subject: CCL: How to select protien for
docking
Sent to CCL by: "james peter" [jp07,sify.com] Hi, My work is on synthetic
chemistry. I have synthesized a series of biologically activ compounds. just I
want to perform protien ligand docking taking my molecules as ligand. My problem
is how can I select a protien and from where I can download a protien. I have
read many tutorials describing method of docking taking an example protien and
ligand. but my problem is how to select a protien from a wide list of protien
structures and how to fit ligand structure into protine for docking. Please help
me so that I can perform docking. Thanking in advance
J.Peter
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