I have made docking using Autodock vina and used Chimera to visualize the results (the docked ligands inside the protein active site). I was able to visualize hydrogen bond interactions, but I need to visualize hydrophobic interactions between hydrophobic parts in the ligand and the protein.
Download this software (DS Visualizer; free) and you can best visualize the hydrophobic interactions in detail.
http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php
Step are:
1. Open the protein-ligand complex.
2. Scripts> ligand interactions> show ligand binding site atoms > CTRL + T
Also you can visualize non-bonded interactions
Download this software (DS Visualizer; free) and you can best visualize the hydrophobic interactions in detail.
http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php
Step are:
1. Open the protein-ligand complex.
2. Scripts> ligand interactions> show ligand binding site atoms > CTRL + T
Also you can visualize non-bonded interactions
You can use Discovery Studio Visualizer, but you need to have a Institution e-mail address for registration at "http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php"
In DS visualizer the steps are as follow:
After opening your structure (ligand-Protein) go to (Menu) Scripts ... > Ligand Interaction ...> show ligand binding site atom
Then go to (Menu) Structure ...> Monitor ...> non-bonded interaction
and from this select the interaction type (Hydrophobic) and from the molecular scope select Intermolecular and OK
Hello Ismail,
Go to UCSF Chimera Tools -> Structure analysis -> Find Clashes/contacts. There by different options available to select required atoms and VDW distances to predict existing non-covalent interactions other than hydrogen bonding.
Best wishes.
SG
Many Thanks, Dr. Satheesh, Your answer was very helpful.
Many thanks for you ALL. The DS visualizer is also a great substitute.
Regards.
Muhammad
Hi,
As hydrophobic interactions are less specific and localized than H-bonds, you really have to use your own expertise in molecular recognition. However, you may be supported by some features embedded in Chimera (e.g. as proposed above, Tools > Structure analysis > Find Clashes/contacts). This will not directly tell you what is the nature of the interaction. You still have to evaluate them yourself with regards to what atoms/residues are involved.
Hope this may help. Good luck.
Antoine.
Protein-Ligand Interaction Profiler (website: https://projects.biotec.tu-dresden.de/plip-web/plip/index) is very good.
using "show hydrophobics" script from PyMOLWiki on pymol itself the hydrophobic can be identified within the specified active site
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