Ideally yes, especially if you have multiple protocols/end points you would like to deliver to your users. There are several ootb BIOVIA packages that create REST services that you can use for reference purpose. Try the apps/scitegic/chemistry package and look at the package.conf files for example.
You can execute individual protocols using the Launchjob service as also described in the RESTful web services guide. For example, the following URL will execute the SHOW ENVIRONMENT protocol, keep the job after completion and run in non blocking mode, so that the service will return the job id. (http://server:port/auth/launchjob?$protocol=protocols/Web Services/Web Port Examples/Generic/Show Environment&$keepJob=t&$blocking=f)