You sure can.
Interspire Website Publisher has a placeholder that allows you to call your own PHP scripts - provided the server has access to that script.
You can either call local or external files, again it depends on the above.
For including from a URL use:
%%Include.http://www.website.com/%%
For including from the local system relative to the Panels folder use:
%%Include.path/from/panels/dir/file.php%%
To specify the absolute path for the include use:
%%Include./absolute/path/script.php%%
If you're not sure what your absolute path is, create a PHP file (e.g. fullpath.php) with this content:
<?php
echo dirname(__FILE__);
?>
Then upload the file to your base Interspire Website Publisher folder and view it from your web-browser. It will tell you what your fill path is.