The partitioning of the energy in ab initio quantum mechanical calculations into its chemical origins (e.g., electrostatics, exchange-repulsion, polarization, and charge transfer) is a relatively recent development; such concepts of isolating chemically meaningful energy components from the interaction energy have been demonstrated by variational and perturbation based energy decomposition analysis approaches. The variational methods are typically derived from the early energy decomposition analysis of Morokuma [Morokuma, J. Chem. Phys., 1971, 55, 1236], and the perturbation approaches from the popular symmetry-adapted perturbation theory scheme [Jeziorski et al., Methods and Techniques in Computational Chemistry: METECC-94, 1993, ch. 13, p. 79]. Since these early works, many developments have taken place aiming to overcome limitations of the original schemes and provide more chemical significance to the energy components, which are not uniquely defined. In this review, after a brief overview of the origins of these methods we examine the theory behind the currently popular variational and perturbation based methods from the point of view of biochemical applications. We also compare and discuss the chemical relevance of energy components produced by these methods on six test sets that comprise model systems that display interactions typical of biomolecules (such as hydrogen bonding and π-π stacking interactions) including various treatments of the dispersion energy.