I need to find intra-molecular interactions within a protein like hydrophobic, electrostatic, and van der Waals interactions. Do you know a program that can find this interactions and how to do that? I am currently using Pymol to visualize the most common residues involved in this type of interactions and measuring the distances, but it is very tedious and difficult.
thank you.
You can use Discovery Studio Visualizer
http://accelrys.com/products/discovery-studio/visualization-download.php
You can use Discovery studio visualizer or Chimera software for this purpose.
For a more deeper analysis I usually use a MM-GBSA calculation + Energy Decomposition analysis in a flavour aimed to find the energetic deteterminants (and the nature of non-bonded interactions) of the protein. With some trick, you can also use the PRIME visualizer tool of the Schrodinger Suite.
Intramolecular Interaction can be visualized by iview-an interactive WebGL visualizer for protein-ligand complex.
or
Autodock
Try MolBridge server
http://nucleix.mbu.iisc.ernet.in/molbridge/index.php use jMol to visualize all the identified interactions
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