You can use GRAMM-X online server or ClusPro 2.0 or flexpepdock server. These are the online servers for protein-protein docking. Alternatively you can also use C-Docker of Discovery Studio but it is a commercial software. Hope this helps.

Best Regards,

Thanks... let me try

Here i suggest you some of the tools and software for protein-protein docking. HEX, ZDOCK,HADDOCK, MOLFIT, DOT, RDOCK among these ZDOCK is best.

you can use chimera

Gold is the best. You can try Molegro as well

You can try with "HPEPDOCK Server "

Gold(Paid software) is best. You can use HADDOCK too....

Hello Muntasir Alam

There are lots of software to perform Docking analysis.

If you peptides for ligand receptor are small, then you can go for Cluspro online tool. But if you need accurate results with details on the energy levels of the resultant docked structure, then i would suggest HADDOCK 2.4 server. Besides, in HADDOCK 2.4, you can specify the interacting amino acids in your sequences (both active and passive), and in case you don't know them, you can get them using CPORT server.

Link for Cluspro server:

https://cluspro.bu.edu/home.php

Link for HADDOCK 2.4 server:

https://bianca.science.uu.nl/haddock2.4/

Link for CPORT server:

https://alcazar.science.uu.nl/services/CPORT/

Hope it helps.

For anyone who might have a similar question, you would find these two papers (links provided below) highly informative. The first paper is a review of available protein-peptide docking methods/tools and it provides a list and brief description of these methods, while the second one is a paper on the benchmarking of several protein-peptide docking methods/tools.

Article Protein–peptide docking: opportunities and challenges

Article Benchmarking of different molecular docking methods for prot...