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Updated: Mar 24, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
Published on: October 15, 2018
Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein-Ligand Binding in
Dmitri G Fedorov1, Kazuo Kitaura2
1Research 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.
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.
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