Structure modeling and molecular dynamics simulation in protein-protein interaction study

Abstract

Protein is a vital macromolecule that contributes to the living system. Functionally, proteins not only work independently, but also form a close network via protein-protein interactions (PPIs), the decisive factor in most biological processes in living organisms. Nevertheless, the study of PPIs has encountered many obstacles due to the lack of experimental structures of the complexes or proteins involved in the interactions. Thanks to the support of bioinformatics tools, methods, and algorithms, the prediction of protein interaction structure has emerged as a potential solution to solve the above difficulties. Molecular docking and molecular dynamics simulation (MDs) are two commonly used methods for predicting PPIs because of their ability to model structure and approximate biological processes, which are consistent with the natural state of the realistic system. Applying these bioinformatics advances has shortened the time, effort, and research costs for scientists. This review provides information on the protein-protein complex structure prediction method and some tools to assist in previous studies. In addition, the force field component of the molecular kinetics simulation method is highlighted, and simulation programs are extensively used.