I'm looking at viral-host protein-protein interactions and have used the HADDOCK web server to dock my host protein and viral protein.
The paper I'm using as guidance for the interface residues simply says that three of the viral protein residues "are involved in hydrophobic interactions". But they don't specify which host protein residues are also involved in these hydrophobic interactions. So, how can I get PyMol to show me which viral protein residues form hydrophobic interactions with the specific host protein residues?
For visualizing 2D PPIs, you may use the DIMPLOT utility of LIGPLOT+ software.
https://www.ebi.ac.uk/thornton-srv/software/LigPlus/download.html
If you're looking at a docking between two proteins, you can check to see which of the interface amino acids are hydrophobic. In the command bar, type: select resn ala, resn trp, resn thr and so on for each hydrophobic amino acid and change the color for easier identification
Thanks so much for your help and suggestions!
I tried those options and some others and decided to go with the PLiP (Protein-Ligand interaction Profiler) web tool because it gave me exactly what I needed. You can find it here: https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index
It allowed me to specify the chains I wanted to see interact and showed me hydrophobic interactions, salt bridges, and ionic interactions, and it let me view the interactions collectively in PyMol.
Dewald Schoeman I recommend biovia discovery studio for all possible interactions; hydrophobic, ionic, aromatic, charges....in addition to hydrogen bonds......with great ease of use. It is obviously necessary to explore a complex product on chimera or autodock or other software.
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