ADL: Docking of phosphorylated peptides

K. Shameer shameer at ncbs.res.in
Thu May 15 10:57:28 PDT 2008


Dear Autodock list,

This is my first mail to the list.

I am working a detailed docking analysis study of phosporylated peptides
with a set of receptors. Currently I am reading the tutorials that
provided in the AutoDock website. I have few questions.

1. I want to dock phosphorylated peptides to a receptor. Is this possible
in Autodock ? If yes, do I need to add any specific charge to my ligand or
receptor ? What are all the steps I should take care to do such a docking
?

2. Which charge is most preffered for protein-peptide docking ?

3. I would like to standardise my protocol using a set of experimentally
solved crystal structures. Before I am starting my docking experiments, I
am planning to take one of these crystal structures (protein-peptide
complexes) seperate the protein and ligand and then perform docking using,
so that I can extrapolate this results to my system. Here I need to dock
the complex in the position of crystal structure. Is there any quick way
to do docking with prior information about docking sites ? In such cases
what are the major points that I should notice to get a docking as good as
the crystal structure ?

Many thanks in advance for any sort of help,
Thanks,
K. Shameer
NCBS - TIFR
Bangalore



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