title: Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein-Ligand Binding in Solution.
abstract: A subsystem analysis is derived incorporating interfragment interactions into the fragment properties, such as energies or charges. The relative stabilities of three alanine isomers, the α-helix, the β-turn, and the extended form are studied and the differences in fragment properties are elucidated. The analysis is further elaborated for studies of binding energies. The binding of the Trp-cage protein (PDB: 1L2Y ) to two ligands is studied in detail. Binding energies defined for each fragment can be used as a convenient descriptor for analyzing contributions to binding in solution.
authors.affiliation: Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST) , Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
authors.forename: Dmitri G
authors.initials: DG
authors.lastname: Fedorov
authors.affiliation: Graduate School of System Informatics, Kobe University , 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Kitaura
mesh_terms: D001665:Binding Sites; D008024:Ligands; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012996:Solutions
chemical_list: D008024:Ligands; D011506:Proteins; D012996:Solutions