Could anyone tell me an alternative to Ligplot+ software which could be used to determine the amino acids and the types of bonding between the interacting amino acids in protein protein interaction analysis?
Academic version of Maestro of Schrodinger package.
https://www.schrodinger.com/maestro
Ramin Ekhteiari Salmas Thanks! I think it is a paid version for full use right?
The things that you want (ligand-protein interactions) is free in this package.
I think it is gonna be self promotion, but you can use MolBridge for finding various interactions....http://nucleix.mbu.iisc.ernet.in/molbridge/index.php
It is available as standalone for Linux OS as well.
Prasun Kumar self promotion or not, I hope it works. Ligplot just does not want to install in my win OS and I am going crazy looking for other options! Thank you very much for the suggestion, but will it work for protein-protein interaction? I can only see options for protein-small molecule interaction.
Protein-Ligand Interaction Profiler here is link https://projects.biotec.tu-dresden.de/plip-web/plip/index
Did any solution help? I am facing the same issue.
Bipasha Bhattacharjee
@ Ishita Shreshtha sorry, nothing really worked for me. youll have to get the ligplot license. I had to get my work outsourced.
@ Bipasha Bhattacharjee you can submit your docked complex to PDBsum under Generate option available in the homepage menu of PDBsum. It will give you ligpot interactions with diagramatic representation for docked complex as well as the residuewise interaction listed with bond distances in the interaction file. Hope this will solve your problem.
@ Rishikesh S. Parulekar This is really helpful, will try it. Thank you!
Discovery Studio Visualizer is really good.
It's also free and easy to install.
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