Re: CCL:starting structure for docking



"nepenthes &$at$& vplaces.net" wrote:
 >
 > Dear CCLers,
 >
 > I hope you will bear with this question of mine but I wasn't able to agree
 with my colleague about it. I've docking a molecule, citrulline, to a protein
 and I obtained the citrulline molecule from a protein-citrulline complex from
 the PDB database website. I think it's suitable by just extracting the
 citrulline sequence and adding hydrogen to it and minimized the structure later
 on before I start my docking process.
 Sounds like you are treating the citrulline as a rigid body. Looks like there
 are at least 5 rotatable bonds in that structure. You should really use
 flexible docking like Autodock. In that case the initial structure does not
 matter, the torsion angles will be randomized during the Monte Carlo steps
 and there should be no bias ... you are effectively performing minimization
 of the ligand during the docking process. Bond length and angle changes are
 probably very minor.
 Richard Gillilan
 MacCHESS