Protocols define a data schema and the contract by which two Decentralized Web Nodes (DWNs) agree to communicate and share data. In other words, protocols define both the data schema and the data permissions as it relates to a certain application or use case.
Protocols are written in a JSON format that is flexible enough to detail what objects are stored as part of the application, as well as who has what permissions on those objects. Although schema and permissions are traditionally decoupled in Web2 development, protocol documents serve as a robust and concise way to define how your application handles data.
Resources
https://developer.tbd.website/docs/web5/learn/protocols#protocol-basics