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Most any vulnerability scanning software that can scan your server would be a step in the right direction. Here are some popular tools:
You will also want to check script security using a tools such as Nikto.
While there is no guarantee that these tools will find all vulnerabilities, obviously you should fix the ones they do find.
For more info on this topic, please visit these SearchSecurity.com resources:
Network Security Tip: Vulnerability scanning with Nessus
Tip: Vulnerability assessment: Leave the scanning to someone else?
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