Notes R5 natively supports full-text indexing of PDF files. I presume that you are going to attach the Acrobat files.
When the database index is created, you have to select the attachments that are to be indexed. Select them to have a binary index, not a raw index.
I just tested this, and it worked as I expected.
It would be a good idea to check this tech note: http://support.lotus.com/sims2.nsf/802ee480bdd32d0b852566fa005acf8d/3ca215f8cabf930d862569d1007fae67
What it basically tells you is that "Indexing for Adobe .PDF files is handled by a third-party filter. It appears that both .PDF versions 1.2 and 1.3 will work, as long as security options are set to "Allow selecting text and graphics" and there is no security password setting." These are security settings that you set when crating the PDF file.
This was first published in July 2001