Hi friends please suggest any server that can show the interactions between protein & ligand (with metal ions, water molecules, cation-pi stacking, pi-pi stacking, hydrogen bonding hydrophobic, any other important druggable interactions)
Server: PoseView (http://poseview.zbh.uni-hamburg.de/)
Free software: LigPlot+ (http://www.ebi.ac.uk/thornton-srv/software/LigPlus/)
Schrodinger Maestro (free if you download from here: http://www.deshawresearch.com/downloads/download_desmond.cgi/)
Only ligand interaction diagram in Schrodinger shows metal interaction.
Thank you very much to all of you (Mahesh Dighe, Ramin Ekhteiriari, Uttampal) for your valuable information. I will go through it and let you know the result.
I like the Ligand-Protein Contact server (LPC-CSU)
http://ligin.weizmann.ac.il/cgi-bin/lpccsu/LpcCsu.cgi
It will give you the amino acids that make contact with each ligand and organize them by contact type.
You can use Discovery Studio and is free software very easy to use
We just published PLIP, a web service and command line tool for characterizing and visualizing all relevant non-covalent interactions between proteins and ligands in PDB structures. The web server is accessible at https://projects.biotec.tu-dresden.de/plip-web . You can also download the source code of the underlying python tool to perform high-throughput analysis locally.
https://projects.biotec.tu-dresden.de/plip-web
http://nar.oxfordjournals.org/content/early/2015/04/14/nar.gkv315.abstract
hello all,
I want to know the importance of the pi-pi stacking interactions and pi-cation interaction of the ligand with the residue with the kinase receptor?
Try BINANA, it creates separate pdb files for the specific interaction types, as well as the particular input scripts for VMD.
You can download BINANA from here: https://git.durrantlab.pitt.edu/jdurrant/binana
Discovery studio visualizer.
https://www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php
You can use following links : https://www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php
Protein-Ligand Interaction Profiler PLIP: http://plip.biotec.tu-dresden.de/plip-web/plip/index
I don't know the server for protein-ligand interaction, but I recommend Ligplus which is one of the best software for analyzing protein-ligand, protein-protein, protein-ions, and protein water interaction. It is very easy and straightforward to use.
https://webs.iiitd.edu.in/raghava/lpicom/index.php
https://structuralbio.utalca.cl/gsp4pdb/#
https://proteins.plus/
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