Using shortcodes in the_content

I am creating a custom API search using Gravity Forms and my theme. I created a filter on the_content() and I was able to successfully change the output of a specific page.

Now I want to use one of my theme’s shortcode elements to make the output look better. Do I set $content = '[shortcode opt=1 opt2=3]'; or is there some different way, maybe by using do_shortcode(). I would test it myself but I don’t want to mess up the script and lose functionality.

Thanks!