Normano: What are you using ?
You should proceed with
great caution before allowing any A/V software "for" Mac OS X Server , to run roughshod over your data, ie: stop and think thrice before allowing it to clobber any DBs you have on that server.
I urge you to take a most critical, even outright cynical view of anything claiming to do so safely.
To date, the
only legitimate concern that is Mac OS X -specific is malware that no software could readily prevent (ie: users knowingly download illegal software, knowingly provide their admin credentials, and knowingly install it).
Past that, we're not anywhere near approaching the merest start of a suggestion of a beginning of a purported possible "need" to scan "OpenDirectory" (ie: the associated OpenLDAP) db files, and you most certainly should not be doing so at any time they are in use (ie: while your server is running).
As far as Mac A/V software goes, I do not use any on any servers I maintain, with the key exception of ClamAV for mail-services. Client-side, I recommend Sophos.