Protein-Protein Interactions Analyzed by the Fragment Molecular Orbital Method.

Protein-Protein Interactions with the Fragment Molecular Orbital Method.

The fragment molecular orbital (FMO) quantum mechanics method offers a comprehensive and computationally inexpensive means of identifying the strength and the chemical nature of the molecular interactions taking place at the protein-protein interface of large biomolecular systems.

Visualization of Properties in the Fragment Molecular Orbital Method Using Facio.

Applications of Integrated Molecular Dynamics and Fragment Molecular Orbital (MD+FMO) Calculations in Drug Discovery and Structural Biology.

This chapter summarizes current evaluation strategies using the MD+FMO approach and integration with diverse experimental techniques, highlighting its value as an analytical method that complements experimental studies in molecular biology.

Theoretical approaches to tracing conformational polymorphism of proteins.

Proteins are not the rigid, static entities as once suggested by early structural biology studies. Instead, they are highly dynamic molecules that are better represented not by a single reference structure, but by a Boltzmann ensemble of conformations. In this article, we review theoretical approaches to reproducing su...

NMR Studies on Protein–Ligand Interactions

How NMR experiments characterize molecular recognition in protein–ligand interactions is discussed, which enables a workflow that accelerates the progression from initial binding identification to structural and dynamic characterization.

Residue-level predictions of the protein-protein interactions of the hepatitis B virus core and envelope proteins

This work predicted the interactions between the capsid (Cp) and envelope proteins (S/M/LHBs) of the hepatitis B virus using a recently established mutation-driven deep-learning model, as well as coevolution signatures that serve as markers of physical interactions and/or functional relationships.