Keeping your heel down through the pedal stroke also helps to better incorporate the glutes.

I've spent the last year, since significantly injuring my knee during an off-bike workout, working on my pedal stroke to engage more muscles throughout. A tight core/straight back coupled with keeping the heel down has been key to much of it.

I've also spent a great deal of time in the weight room doing squats, V-squats, deadlifts, lunges, leg presses and leg curls, as well as a variety of exercises to strengthen my hip flexors. I avoid leg extensions as they overtax my knee. And with the leg curls, I do them individually, which is significantly more difficult.