Molecular Docking

Question

[Rishika Sengupta]

My PDB file contains the enzyme along with the substrate(HetAtom). How do I visualise the active site along with the substrate?

I am working on Linux platform and have installed Autodock 4 along with PMV.

Please advice.

Thanks

Rishika Research Engineer CARLBio Group

[Khader Shameer]

Have you done docking experiments prior to visualization ? It should be relatively easy to visualize your docked complexes within AutoDock (ADT[AutoDockTools] http://autodock.scripps.edu/downloads/resources/adt/index_html) or any macromolecular visualization tools like PyMoL or RasMol.

[Rishika Sengupta]

After I load the pdb file(along with the substrate) in PMV or ADT, how do I highlight the active site and visualise the substrate bound to it?

[Khader Shameer]

If you are looking at a well studies structure, you can either do a literature search to find key active site residues or use databases like Catalytic Site Atlas http://www.ebi.ac.uk/thornton-srv/databases/CSA/ to find your active site residues. If you are looking at a homology model with not much of prior information, you have to perform a structure-based-sequence alignment to see the conserved residues/motifs and define your active site residues. See this work from my graduate lab for example: http://www.ncbi.nlm.nih.gov/pubmed/19763327

[Khader Shameer]

Please see my detailed answer on how to high-light active site. If you could properly edit your question with a well-defined title (for example "visualizing active site") you may get better responses.

Answer 1

[Vladimir Chupakhin]

Try autodock vina - is more easy to use.

[Michael Schubert]

I second Vina. See http://wwwuser.gwdg.de/~dseelig/adplugin for a PyMOL plugin (though AudoDockTools will do as well)

[Rishika Sengupta]

The PDB file contains the hetatom(substrate). How do I visualise the active site of the enzyme along with the bonded substrate?

Answer 2

[Woa]

The Autodock module within Yasara( Commercial software) works like a charm

[Rishika Sengupta]

Could not use it since the docking part is commercial

Answer 3

[Khader Shameer]

If you are looking at a well studies structure, you can either do a literature search to find key active site residues or use databases like Catalytic Site Atlas to find active site residues.

If you are looking at a homology model with not much of prior information, you have to perform a structure-based-sequence alignment to see the conserved residues/motifs and define your active site residues. See this work from my graduate lab.

For visualization options see LIGPLOT and answers discussed here and here.

[Rishika Sengupta]

Since I am using known literature information, I know the active sites of the enzymes. LIGPLOT showed the interactions while Catalytic Site Atlas gave the residue information. Thanks a tonne... Regards Rishika