This review paper is based on the lecture presented in Kyoto on August 25th, 2012, by one of the authors (HC) in the Memorial Symposium for the 50th Anniversary of the Hansch-Fujita Approach; however, several parts have been added. The current paper contains (I) a formulation of an extended one of the well-known Hansch-Fujita QSAR analysis, but a new promising one (called linear expression by representative energy terms (LERE)-QSAR), which can consider ligand-protein interactions explicitly by using modern molecular calculations on a whole ligand-protein complex, and (II) applications of the LERE-QSAR analysis to several cases.