I want to visualize the interaction between a protein and a peptide, can I use Pymol? I have the PDB file for both
Do you have a PDB file of the complex?
If not, you might want to first want to dock the peptide to the protein, e.g using CABS-dock http://biocomp.chem.uw.edu.pl/CABSdock, FlexPepDock http://flexpepdock.furmanlab.cs.huji.ac.il , HPepDock http://huanglab.phys.hust.edu.cn/hpepdock/, MDockPep http://zougrouptoolkit.missouri.edu/mdockpep/
to name just a few of the most recent servers.
Once you have a structure or reasonably reliable model of the complex, you can start to analyze the interaction between protein and peptide. In PyMOL, the "within" operator is your friend. If you have two selection S1 (eg. your protein) and S2 (e.g your peptide), the command
select contacts1, S1 within 3.6 of S2
will select all protein atoms within 3.6 Å of the peptide (ca. C-C VdW contact)
For more on how to use selection commands in PyMOL, see https://pymolwiki.org/index.php/Selection_Algebra and my "Intermediate PyMOL" presentation. Presentation Intermediate PyMOL
.My favorite piece of software to catalog interactions is the Protein-Ligand Interaction Profiler (PLIP) https://plip.biotec.tu-dresden.de/plip-web/plip/index.
However, the web server recognizes the ligand as being the Heteroatom component of the PDB file. If you want to use it to profile the interactions between a protein and a peptide, you have to download the program and install it locally.
With the local installation, you can explicitly define the peptide you want to consider as ligand.
"For the detection of ligands, PLIP relies on the separation of ATOM and HETATM entries in the PDB file.
The latter are searched for suitable ligands when running in normal mode.
Peptide ligands, however, are usually deposited as ATOM entries in a separate chain.
PLIP can not detect these entities automatically.
To switch into protein-peptide interaction mode, start PLIP with the option `--peptide`, followed by the peptide chain of interest, e.g.:
bash
plip -i 5hi4 --peptides I -vx
or you may use LIGPLOT plus for interaction study, follow the link provided below
https://www.ebi.ac.uk/thornton-srv/software/LigPlus/
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