In silico tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides. However, restricted sampling of both ligand and receptor conformations and use of approximated scoring functions can produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) can provide valuable information in deciphering functional mechanisms of proteins/peptides and other biomolecules, overcoming the rigid sampling limitations in docking analysis. This review will discuss the information related to the traditional use of in silico models, such as molecular docking, and its application for studying food proteins and bioactive peptides, followed by an in-depth introduction to the theory of MDS and description of why these molecular simulation techniques are important in the theoretical prediction of structural and functional dynamics of food proteins and bioactive peptides. Applications, limitations, and future prospects of MDS will also be discussed.

In recent decades, bioactive peptides have become an emerging field of interest in the scientific community as well as the food, pharmaceutical, and cosmetics industries. A growing body of research indicates that consumption of bioactive peptides may play a vital role in health through their broad spectrum of bioactivity such as antioxidant, antihypertensive, antimicrobial, anti-inflammatory, immunomodulatory, and anti-proliferative activities. In addition, bioactive peptides can be used as food preservatives due to their antimicrobial and antioxidant activities. However, some factors limit their nutraceutical and commercial applications, including easy chemical degradation (e.g., pH, enzymatic), food matrix interaction, low water-solubility, hygroscopicity, and potential bitter taste. Bearing that in mind, the encapsulation of bioactive peptides in different materials can help overcome these challenges. Studies have demonstrated that encapsulation of bioactive peptides increases their bioactivity, improves their stability, sensory properties, increases solubility, and decreases hygroscopicity. However, there is limited scientific evidence about the bioavailability and food matrix interactions of encapsulated peptides. Besides, the diverse colloidal systems used to encapsulate bioactive peptides have shown stability and good encapsulation efficiency. This review provides an overview of current advances in the encapsulation of bioactive peptides, considering the technology, developments, and innovations in the last lustrum.