chapter 1 Introduction / chapter 2 Theoretical Background of the Fragment Molecular Orbital (FMO) Method and Its Implementation in GAMESS / chapter 3 Developments of FMO Methodology and Graphical User Interface in ABINIT-MP / chapter 4 Excited States of Photoactive Proteins by Configuration Interaction Studies / chapter 5 The Fragment Molecular Orbital–Based Time- Dependent Density Functional Theory for Excited States in Large Systems / chapter 6 FMO-MD: An Ab Initio-Based Molecular Dynamics of Large Systems / chapter 7 Application of the FMO Method to Specific Molecular Recognition of Biomacromolecules / chapter 8 Detailed Electronic Structure Studies Revealing the Nature of Protein–Ligand Binding / chapter 9 How Does the FMO Method Help in Studying Viruses and Their Binding to Receptors? / chapter 10 FMO as a Tool for Structure-Based Drug Design / chapter 11 Modeling a Protein Environment in an Enzymatic Catalysis: A Case Study of the Chorismate Mutase Reaction