FAQ: Is it safe to search with secret chemical structures over the web?
The short answer is maybe. It depends on your corporations/organisations confidentiality policies, whether you have spyware on your computer, whether someone is recording your network traffic, etc. We (the EMBL-EBI) will do nothing to store, analyse, disclose or otherwise publish any chemical structure queries, but fundamentally the searches are performed over the internet with the http protocol (as opposed to the encrypted https protocol).
We are investigating the implementation of a secure server currently (November 2009).