PouchDB as a real live data tool for different collections-open source projects pouchdb/pouchdb
Yep, PouchDB works fine for real-time stuff. It doesn’t use web sockets, but it uses long-polling, which is fast enough for most use cases.
It sounds like you probably should create a separate database for each paper, assuming you want to restrict access on a per-paper basis. CouchDB authentication is kinda tricky, but basically if you want to control read access, you can either give users full read access or zero read access to an entire database. There’s a writeup here.
Also don’t worry about creating thousands of databases; a “database” is cheap in CouchDB.
The only other thing I would advise is that maybe you would like the relational-pouch plugin, because then you could easily set up a relational-style database with a “paper” type and a “comment” type.