Ligand Structure Looks Different - After Docking

Question

[Sathish]

Dear all,

Am using autodock 4.2, after docking my compound structures looks different in complex (protein -ligand). I want to know why my compounds looks like this?

i have prepared ligand and checked the following methods.

1. Downloaded from pubchem/kegg - directly given as input
2. Downloaded from pubchem/kegg - Energy minimized then given as input
3. Drawn structure - directly given as input
4. Drawn structure - Energy minimized then given as input

Energy minimization(EM) was performed separately in two ways, (i) docking server (MMFF94 and Gasteiger charges at PH 7) and (ii) Charmm (DS 3).

each structures was given separately to perform docking.

While analysis the ligand structures looks different, ligand structures (few) attached along with this post.

Please give your valuable suggestions... Thanks in advance....!

http://www.freeimagehosting.net/54222

Sathish

[Vladimir Chupakhin]

what kind of docking software did you use? Provide also link to the pubchem compound

[Vladimir Chupakhin]

From my opinion it seems that (1) your visualization software wrong or (2) docking behave incorrectly, (3) or input structure incorrect.

Answer 1

[João Rodrigues]

Dear Sathish,

Like chupvl said, the weird look of the structures is from bad representation of bonds in the visualization software. This might also mean that the atoms are too close .. Try representing the structures with spheres and setting the spheres scale to a small enough value. For example in Pymol:

*show spheres*
*set sphere_scale, 0.3*

Then measure some distances between these atoms and see if they make sense.

As for the structures looking different, I guess it's normal since during docking they are minimized to adapt to the protein.

Answer 2

[Flow]

Basically, no docking program can predict docking with 0.0000000 angstrom RMSD