MAS2HP: A Multi Agent System to predict protein structure in 2D HP model

Protein Structure Prediction (PSP) is an unsolved problem in the field of computational biology. The problem of protein structure prediction is about predicting the native conformation of a protein, while its sequence of amino acids is known. Regarding processing limitations of current computer systems, all-atom simulations for proteins are typically unpractical; several reduced models of proteins have been proposed. Additionally, due to intrinsic hardness of calculations even in reduced models, many computational methods mainly based on artificial intelligence have been proposed to solve the problem. Agent-based modeling is a relatively new method for modeling systems composed of interacting items. In this paper we proposed a new approach for protein structure prediction by using agent-based modeling (ABM) in two dimensional hydrophobic-hydrophilic model. We broke the whole process of protein structure prediction into two steps: the first step, which was introduced in our previous paper, is about biasing the linear sequence to gain a primary energy, and the next step, which will be explained in this paper, is about using ABM with a predefined set of rules, to find the best conformation in the least possible amount of time and steps. This method was implemented in NETLOGO. We have tested this algorithm on several benchmark sequences ranging from 20 to 50-mers in two dimensional Hydrophobic-Hydrophilic lattice models. Comparing to the result of the other algorithms, our method is capable of finding the best known conformations in a significantly shorter time. A major problem in PSP simulation is that as the sequence length increases the time consumed to predict a valid structure will exponentially increase. In contrast, by using MAS2HP the effect of increase in sequence length on spent time has changed from exponentially to linear.