martinibuster - 1:47 am on May 21, 2012 (gmt 0)
You can't put an antivirus on your server to protect you. The issue is software on your server that is out of date and has vulnerabilities. It can be anything from Plesk, WordPress, Joomla, vBulletin, etc. The best that can be done is to make sure everything installed on your server is up to date.
Additional tasks can be to download your site and review key pages like the home page for iframes that you didn't put there. If the site has PHP includes then take a peek at some of the top level pages (like headers and footers) to see if there have been any changes there.