Please suggest suitable online platform for protein-protein docking? and analyzing its results?

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Bruno Di Geronimo

Hello, here you have link in which some of the most popular pp docking online softwares are summarized:

http://www.vls3d.com/links/bioinformatics/protein-protein-interaction/protein-protein-docking

Among all of them, I recommend pyDock from Barcelona Supercomputer Center.

Hope this helps, best regards

Nayim Sepay

My suggestion is HADDOCK. It is best. The link is given below.

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

Jitendra Kuldeep

after performing docking with cluspro if you find that the proteins are separated then probably you have done some mistake in the process.

Regarding the binding affinity score, after docking is finished it shows the score in the link itself.

My suggestion is you can try once again and review you results.

Anamika Gupta

Thankyou for the reply

Jitendra Kuldeep I have tried to do docking of receptor protein and ligand-protein.

Refined its structure in discovery studio. and than uploaded on cluspro.

After docking s complete, I got both proteins separated even after docking. I can see both proteins separated.

where I can be wrong.

As the proteins which I have selected has multiple chains. So the desired chain I have kept and deleted the rest chains.

Binding affinity score is not there on cluspro. It only displays coefficient score of balanced, electrostatic, etc.

I am not able to understand where I am wrong.

And moreover, I want to know that where I can visualize my results and get interacting amino acid, bonds, RMSD values.

As I have tried using Pymol (whcih I am unable to understand).

can you please suggest some other software where I can visualize interaction.

as I have done protein-ligand docking visualization using discovery studio only where it was very easy to get all the interacting bonds.

So can you please suggest some software or paper which I can follow.

Regards

Anamika

if you want to visualise the docking results like you did in discovery studio visualiser, I would suggest you to download and install the academic version of Schrödinger maestro software. It gives a very nice plot, you can try it.

Regarding protein protein docking using cluspro and the analysis of docking result you can follow this paper:

Gaurav S, Ranjan R, Kuldeep J, Dhiman K, Mahapatra PP, Ashish, Siddiqi MI, Ahmed S. The N-terminus region of Drp1, a Rint1 family protein is essential for cell survival and its interaction with Rad50 protein in fission yeast S.pombe. Biochim Biophys Acta Gen Subj. 2021 Jan;1865(1):129739. doi: 10.1016/j.bbagen.2020.129739. Epub 2020 Sep 19. PMID: 32956753.

Hope it may be helpful for you.

Hi Arijit, for protein-protein interaction plot you can check Ligplot "https://www.ebi.ac.uk/thornton-srv/software/LigPlus/". Maybe this can solve your problem.