What in your opinion is the "best" software for protein pockets detection? Do you have any link to a review or benchmark on software for protein pockets detection that I can read ?
you Q-site finder and Active site finder http://www.scfbio-iitd.res.in/dock/ActiveSite.jsp according to Anita Tripathi is right but according to your ligand you want to find the pockets then you can prefer the auto vina for analyzing the binding pockets
Never depend on any one server as all of them are based on different approaches. Normally i compare results of Castp & pocketFinder. Both of two servers give you idea of pockets i.e. of probable enzymatic sites and not of exact enzymatic sites!!! For exact enzymatic site try PDBsum or CAS (on EBI server), you can get results on these servers if enzymatic site has been reported by any scientist (they dont follow any bioinformatics approach to predict, if know they will tell you).
So best approach is to compare results of Castp, PocketFinder, PDBSum & CAS to conclude best pocket (which can turn into enzymatic site!!!).
And if you are working with Castp& PocketFinder then you don't need to run on any other servers could be Qsitefinder, Fpocket etc.
Also if you are using these sites for docking, then always use more then one site for docking you dont know where you ligand can bind in much better way!! Its more or less like hit-n-trial method.
Hi Benjamin, we have recently developed a protein pocket detector using convolutional neural networks (DeepSite, link to paper here: Article DeepSite: Protein binding site predictor using 3D-convolutio...
). In case you are looking for cryptic pockets (this is, invisible in apo structures), I suggest giving a try to CrytoScout. Both applications are available free of charge in the PlayMolecule webserver (www.playmolecule.org).
Hi Ben, you can compare a few reliable programs as professional people mentioned above, while CASTp is definitely the good one. Now we updated CASTp to the new 3.0 release with more valuable information, and more user-friendly also. Please check with our server at: http://sts.bioe.uic.edu/castp