Estimating the kinetics of electron transfer (ET) processes in biologically relevant systems using theoretical-computational methods remains a formidable task. This challenge arises from the inherent complexity of these systems, which makes it impractical to apply a fully quantum-mechanical treatment. Hybrid quantum mechanical/classical mechanical computational approaches have been devised to enable the explicit simulation of electron transfer kinetics. This concept article focuses on a specific theoretical-computational method employed in this context, namely the Perturbed Matrix Method (PMM), which has the merit of being able to include large-scale conformational effects in the ET kinetics and potential multiple, alternative, ET channels. We describe its underlying physical principles, examine its advantages and limitations, and offer insights into its applications. Examples of the approach are discussed in the context of estimating photo-induced electron transfer kinetics in proteins. The non-exponential behavior observed in the presented case studies arises mainly from an active coupling with the environment fluctuations, but partly also stems from the presence of branching ET pathways.