When many runners consider muscle groups directly affecting knee stability, alignment and thus pain, thoughts turn to the glutes (externally rotating and abducting the hip) and quads (particularly VMO).
It is important however that we don’t overlook the hamstrings and adductors.
Dynamic imbalances between quads:hams and adductors:abductors play an important part in influencing knee stability and patellofemoral alignment during functional movement patterns such as running.
Below are a couple of videos showing two hamstring biased variations of a simple bridging exercise, which also affects the long adductors.
We use these two variations as two of the more basic exercises in our hip strengthening knee rehab program.