The Interactome of Protein, DNA, and RNA

Abstract

Proteins participate in many processes of the organism and are very important for maintaining the health of the organism. However, proteins cannot function independently in the body. They must interact with proteins, DNA, RNA, and other substances to perform biological functions and maintain the body's health. At present, there are many experimental methods and software tools that can detect and predict the interaction between proteins and other substances. There are also many databases that record the interaction between proteins and other substances. This article mainly describes protein-protein, protein-DNA, and protein-RNA interactions in detail by introducing some commonly used experimental methods, the software tools produced with the accumulation of experimental data and the rapid development of machine learning, and the related databases that record the relationship between proteins and some substances. By this review, we hope that through the analysis and summary of various aspects, it will be convenient for researchers to conduct further research on protein interactions.

Keywords: ChIP; Co-immunoprecipitation (Co-IP); Deep Learning; Electrophoretic Mobility Shift Assay (EMSA); EuRBPDB; Network Analysis; Protein Data Bank (PDB); Protein–DNA Interaction; Protein–Protein Interaction; Protein–RNA Interaction; Proximity Labeling; STRING; Yeast Two-Hybrid.