Computational Modeling of Proteins based on Cellular Automata

The literature of building computational and mathematical models of proteins is rich and diverse, since its practical applications are of a vital importance in the development of many fields. Modeling proteins is not a straightforward process and in some modeling strategies, it requires to combine concepts from different fields including physics, chemistry, thermodynamics, and computer science. The focus here will be on models that are based on the concept of cellular automata and equivalent systems. Cellular automata are discrete computational models that are capable of universal computation, in other words, they are capable of doing any computation that a normal computer can do. What is special about cellular automata is its ability to produce complex and chaotic global behavior from local interactions. The paper discusses the effort done so far by the researchers community in this direction and proposes a computational model of protein folding that is based on 3D cellular automata. Unlike common models, the proposed model maintains the basic properties of cellular automata and keeps a realistic view of proteins operations. As in any cellular automata model, the dimension, neighborhood, boundary, and rules were specified. In addition, a discussion is given to clarify why these parameters are in place and what possible alternatives can be used in the protein folding context.