Multi-agent Systems Applied in the Modelling and Simulation of the Protein Folding Problem Using Distributed Constraints

摘要

The protein folding problem is one of the most challenging problems in current biochemistry and is an important problem in bioinformatics. All current mathematical models of the problem are affected by intrinsic computational limits. The previous research offers few approaches that make use of multi-agent systems to resolve this problem. In this paper we present an agent-based framework for protein structure prediction, composed by autonomous agents which collaborate in order to find a solution using Distributed Constraint Programming (DisCSP/DisCOP). Each amino acid of an input protein is viewed as an autonomous agent that communicates with others by transmitting messages. In this article was analysed the NetLogo environment with the purpose of building a general model of implementation and simulation for the protein structure prediction. Starting from the proposed implementation model with lattice models based on distributed constraints, in this article we present a multi-agent systems which can be used for the implementation and simulation of the protein structure prediction, that can run on a single computer or on a cluster computing environment. The version of the tool presented herein allows studying and exploring complex problems belonging principally to structural biology, such as protein folding.