I have a protein-protein complex and therefore, need a visualiser to look at those amino acids which are at interface of these proteins. However I am also interested to see the interactions between the amino acids of these concerning proteins. For that, I tried MOE, Discovery studio Visualiser and Pymol but couldn't achieved the purpose. May be I am lacking somewhere.
Could somebody tell me, any window based visualiser which could be used for visualising the interactions of these amino acid present in concerning protein?.
An appropriate viewer for windows version is vmd:
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
Unless you have inhibitions in submitting your structure online, PDBSum should be a good server to use. While it already has details on proteins at the interface for the structures in PDB, you could also submit your structure and it returns you an array of details about your structure which includes the residues at the interface.
I believe Chimera too does it in a crude manner but I find PDBSum the best (of the ones I used).
You can try VMD or YASARA, both are relativelly user friendly.
In my experience YASARA is more intuitive, and VMD is significantly more powerfull.
Thanks Chris and Orts, but could you please suggest me some papers or manual for doing so, as I already tried VMD before.
You need to search the user´s manual, and look about the task you want to perform in that viewer.
VMD is a extensive software, probably you will need search something more than a basic manual. Anyways, the basic about VMD you can find there here:
http://www.ks.uiuc.edu/Research/vmd/current/ug/
Run you protein models (PDBs) through the PDBePISA web server.
http://www.ebi.ac.uk/pdbe/pisa/
Go there, hit lunch PDB3Pisa button, enter your coordinates.
It will do everything you can imagine to characterize a protein-protein interface and more.
Protein–protein interactions refer to physical contacts established between at least two proteins. This can result in the formation of complexes. Although we have a multitude of techniques to study the interaction, to characterize the interacting surfaces we need 3D models of the complex by X-ray crystallography, NMR or MD. The 3D information contained in the complex enables the construction of residue interaction networks (RIN) similar to metabolic or genetic ones but having residues as nodes instead that proteins or genes. These networks can predict key structural or functional residues in proteins (HUB residues), interacting residues, and much more, based on statistical parameters used in graph theory such as the closeness centrality and betweenness centrality values for each residue. To simplify the difficult task of visualize RIN have also been developed specific visualization tools. Cytoscape, for instance, is an open-source software widely used and lots of plugins are currently available for the calculation of various structural and networking parameters.
You can use the CoCoMaps webserver. It lists the interacting residues and you can download a .pml file to visualize the results in PyMOL.
https://www.molnac.unisa.it/BioTools/cocomaps/
Don't you have in Discovery Studio Visualiser "Non-bond interactions" option? I have it on the upper tool panel, but I'm not sure that it was there from the beginning, probably it is because I use it a lot. Try to look also in "Receptor-Ligand interactions" menu.
I agree with Facundo Orts. YASARA can be used for the purpose in a user friendly way. You can also look at PDBsum in the protein interaction tab.
Discovery studio is the best visualizer and it has some script to analize your interaction
Maybe you can try to use Maestro in Schrodinger software or VMD. By using these visualizers, maybe you can analize the protein-protein interactions among the key amino acids.
Use Pymol. Load the complex, go to Action [A] and do find--------> polar contacts
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