I have novel peptide sequences of 20-30 AA in length. I need to dock it with antigenic proteins. I have to do blind docking of the protein and peptide. I used Cluspro for which I predicted the structure of peptide in pepfold server. Is it good to use the server that needs peptide structure as input or peptide sequence as input for blind docking? Which one is reliable?
Dear Suba Venkat ,
Not familiar with Cluspro but after reading some info about it I am under the impression that you need pdb files (or other coordinate info) of both your protein and peptide. According to a somewhat older paper, I-Tasser is better than Pep-fold: https://onlinelibrary.wiley.com/doi/abs/10.1002/psc.1410 so you might consider to try I-Tasser as well: https://zhanglab.dcmb.med.umich.edu/I-TASSER/
Best regards.
For peptide modeling, yes, PEPFOLD is reliable. Just increase the number of simulations to 200.
Moreover,
1. If you don't know the binding pocket information (where to dock), you can use CABSdock
http://biocomp.chem.uw.edu.pl/CABSdock
2. Else, if you know some interacting residues in antigenic protein (you can identify from any related structural data in PDB, for instance), then you can use HPEPDOCK
http://huanglab.phys.hust.edu.cn/hpepdock/
3. Or you can even use the recently published InterEvDock3, which uses covariation-based contact maps (evolutionary information).
https://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock3/
4. Also, for high-resolution peptide docking refinement, you could use
http://flexpepdock.furmanlab.cs.huji.ac.il/
I hope, these servers can work for you. Thanks
dear suba,
try this server: https://wenmr.science.uu.nl/haddock2.4/submit/1 ...and you can visulized the results by Chimera1.14
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