search

ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
561 stars 199 forks source link

Is AutoDock-Vina applicable to peptides? #302

Open SoodabehGhaffari opened 2 months ago

SoodabehGhaffari commented 2 months ago

Hello, I was wondering if I can use AutoDock-Vina for docking between proteins and peptides.If not, do you have other suggestions?

Best Regards Soodabeh

rwxayheee commented 2 months ago

Hi @SoodabehGhaffari In AutoDock Suite there is a project specialized in docking peptide ligands - AutoDock CrankPep (ADCP). You can compare them method-wise, try a few peptide ligands of your own, visualize the outputs and check the ranking.

Just a user's opinion here - For short peptides (some 5-9 AA peptide ligands I designed, which barely form a large piece of any secondary structure) I had positive experiences docking them using AutoDock Vina. I got similar top-scored poses in AutoDock Vina and ADCP, but at the moment AutoDock Vina is so much faster. I'm less experienced in docking longer peptides, though.. Maybe you could also ask in a bigger computational chemistry community that are not exclusive to AutoDock :>

diogomart commented 2 months ago

I agree with @rwxayheee. As for further suggestions, if you have only standard amino acids, software for protein structure prediction might be useful, e.g. Alphafold, Rosetta, RFdiffusion.

eunos-1128 commented 1 month ago

@SoodabehGhaffari

In addition to conventional softwares for protein structure prediction, AlphaFold2-multimer could be worth trying.

According to this paper AF2-multimer outperformed other methods in case of peptide/protein docking. (Note that AF2-multimer needs you to input sequence data instead of structure data like PDB)