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
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Rishika Sengupta •
Try autodock vina - is more easy to use.
I second Vina. See http://wwwuser.gwdg.de/~dseelig/adplugin for a PyMOL plugin (though AudoDockTools will do as well)
The PDB file contains the hetatom(substrate). How do I visualise the active site of the enzyme along with the bonded substrate?
Could not use it since the docking part is commercial
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.
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Khader Shameer
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
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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.
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?
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
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.