e.g. to replace a bunch of files in a folder which end in .pdb, and change the extension to .txt, run:
find . -iname "*.pdb" -exec bash -c 'mv "$0" "${0%\.pdb}.txt"' {} \;
Note: The website above says it does this "recursively" by which they may mean it acts on subfolders, too. I haven't tested this, so be careful!