Hi Sidrah Jahangir

You can take the entire list of proteins obtained from mass spec and use the STRING's website (https://string-db.org/). The maximum limit I think is around 2000. In the settings section, you can edit the minimum required interaction score: highest confidence (0.900). You can also edit max number of interactors to show: no more than 5 or 10 and UPDATE the analysis. Again under active interaction sources: choose Experiments or whichever is convenient to you.

You can also use Cytoscape as suggested by Suresh Kumar . You have plugins such as clueGo, STRING, EnrichmentMap which can allow to study the PPI.

Hope this helps!

Varsha

Rosetta codes can be useful....If you run on multiple PDBs you can use a simple loop in any program (Python, C++ or FORTRAN)

If you run on multiple PDBs you can use a simple loop in any program (Python, C++ or FORTRAN)

https://www.rosettacommons.org/software

Dear Sidrah Jahangir

There are many ways to support you for performing such amazing project. If you have a basic knowledge of working with python scripts, paying attention to the content of GitHub website can provide some functional python scripts for your purpose. This URL: https://github.com/topics/protein-protein-interaction?l=python includes various codes for handling your query. However, if you would like to apply a stable and standalone software for your work, I highly recommend you to follow the instruction of Ingenuity Pathways Analysis (IPA) tool for gaining a deep learning about the possible interaction of the target proteins. However, PSOPIA bioinformatics tool: https://mizuguchilab.org/PSOPIA/ also provides a simple protocol to check the possible interactions between different types proteins by using the sequence of these queries.