Not able to view the downloaded model from ClusPro using PDBSum. Since both the docked proteins contain single A chain, PDBSum shows it as single image. Please give suggestions. Also tried to save the chains as separate using PyMol, still didn't work.
I think with the help of LigPlot+, you can see the 2D protein-protein interaction.
But in any case, you have to change the chain identifier of one of the proteins. you can manually edit the chain identifier directly in the PDB file using a text editor. Locate the lines that define the chain identifier and change the chain identifier accordingly. Save the modified PDB file after making the changes.
Please rename the Chain ID (Such as A and B ) of the selected docked complex using PyMol and submit it to the PDBSum server.
Visualizing the interactions in the protein-protein docked model obtained from ClusPro can be done using popular molecular graphics systems such as molecular visualization software, 'PyMOL', followed by 'Discovery Studio Visualizer'.
A complex structure obtained from ClusPro may have multiple HEADER records, which will prevent opening the structure directly in Discovery Studio. So, to make the complex suitable for opening in Discovery Studio Visualizer, open the docked model in PyMOL and export the image and save it as 'yourfile.pdb'. Use the File menu to 'Open' and 'Export' the PDB file. The exported file can be opened in Discovery Studio.
Once you have loaded your docked model in Discovery Studio, you can visualize the interactions using the 'Hierarchy' file under the 'View' menu.
Change the structural view using the 'Display Style' menu and select 'HBonds' from 'Non-Bond Interactions' to view the interactions. This will help us visualize the interacting molecules/amino acid residues between the docked proteins. Details of bonds including bond distance, bond type, etc. can also be recorded using the tool.
Hope this helps you…..
- Badges
- Science topic
- Similar topics
- Filing