As far as I know, there are at least two docking tools that can be used for protein docking studies, namely the HDOCK server and the ClusPro server. However, I don't know how to validate the binding pocket of the target protein used, so how do I do that? Is it possible to use blind docking? If yes, how to do it? Thank you in advance.
Best Approach would be identify top 5 binding pockets in both the proteins you are planning to dock using MetaPocket or SiteID or PocketFinder tool.
After that do some literature review, if any wet lab experiments support predicted binding pockets for interactions.
Then try to use these binding pockets to run Docking using either HADDOCK, ZDOCK, CLUSPRO, HEX or other protein protein docking methods.
The second step of literature review is highly important as it provide some basis of your study.
Further MD studies can be performed to check the stability of the Docked complex.
regards
Tanuj
Dear Ahmad Dzulfikri Nurhan you can use Patchdock (https://bioinfo3d.cs.tau.ac.il/PatchDock/php.php) and FireDock (https://bioinfo3d.cs.tau.ac.il/FireDock/php.php) tools for protein-protein docking and the second thing that you want binding site of the receptors..so for that you have read the research paper of the same paper..otherwise, you can use Deepsit server ( https://www.playmolecule.org/deepsite/).
And the third thing for result validation please mention your problem or you can read the paper as much as you regarding the problem.
best wishes.
There are several tools for protein protein docking as already mentioned by Aqib Sarfraz and Tanuj Sharma . You can even use AutoDock/Vina. And you can use blind docking. For method validation, you need positive control. You can take known protein protein complexes from PDB and run self docking to check if the method/software tool can reproduce the binding pose. In positive control, choose proteins which are similar to your protein of interest (maybe a complex of your target protein with some other protein). For result "validation" you need experiment. Without some experimental data, in silico results shall always remain a prediction.
Look at the latest results of the CAPRI docking contest for the performance of various docking algorithms and various tools for clustering and re-scoring of docking results
https://www.capri-docking.org/resources/
Dear Tanuj Sharma Aqib Sarfraz Uttam Pal Annemarie Honegger , I'll try to conduct the protein-protein docking according to your suggestions... I hope, I can do as great as you do... thanks in advance from Indonesia :)
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