Is it still safe to check data on MD5 sum?

For this purpose absolutely. The collision attack that was discovered against MD5 means that some very smart people have managed to create two different bits of data which produce the same MD5 hash. The creation of a modified file the MD5 of which matches that of an existing, "real-world" file is as yet only theoretically possible. And the chance of this happening by accident on your machine is less than that of your server, all backups and your pants spontaneously combusting :-).