Multi-Agent Systems Applied in the Modeling and Simulation of Biological Problems: A Case Study in Protein Folding

Multi-agent system approach has proven to be an effective and appropriate abstraction level to construct whole models of a diversity of biological problems, integrating aspects which can be found both in "micro" and "macro" approaches when modeling this type of phenomena. Taking into account these considerations, this paper presents the important computational characteristics to be gathered into a novel bioinformatics framework built upon a multiagent architecture. The version of the tool presented herein allows studying and exploring complex problems belonging principally to structural biology, such as protein folding. The bioinformatics framework is used as a virtual laboratory to explore a minimalist model of protein folding as a test case. In order to show the laboratory concept of the platform as well as its flexibility and adaptability, we studied the folding of two particular sequences, one of 45-mer and another of 64-mer, both described by an HP model (only hydrophobic and polar residues) and coarse grained 2D-square lattice. According to the discussion section of this piece of work, these two sequences were chosen as breaking points towards the platform, in order to determine the tools to be created or improved in such a way to overcome the needs of a particular computation and analysis of a given tough sequence. The backwards philosophy herein is that the continuous studying of sequences provides itself important points to be added into the platform, to any time improve its efficiency, as is demonstrated herein. Keywords—multi-agent systems, blackboard-based agent architecture, bioinformatics framework, virtual laboratory, protein folding. Dr. Hiram Isaac Beltrán* (corresponding author), Departamento de Ciencias Naturales, DCNI, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Pedro Antonio de los Santos 84. Col. San Miguel Chapultepec. Miguel Hidalgo 11850. México, D.F. e-mail: hbeltran@correo.cua.uam.mx. Tel. +52 (55) 26363853. Dr. Arturo Rojo-Domínguez, Departamento de Ciencias Naturales, DCNI, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Pedro Antonio de los Santos 84. Col. San Miguel Chapultepec. Miguel Hidalgo 11850. México, D.F. e-mail: arojo@correo.cua.uam.mx. Máximo Eduardo Sánchez, Departamento de Matemáticas Aplicadas y Sistemas, DCNI, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Pedro Antonio de los Santos 84. Col. San Miguel Chapultepec. Miguel Hidalgo 11850. México, D.F. Dr. Pedro Pablo González* (corresponding author), Departamento de Matemáticas Aplicadas y Sistemas, DCNI, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Pedro Antonio de los Santos 84. Col. San Miguel Chapultepec. Miguel Hidalgo 11850. México, D.F. Tel. +52 (55) 26363805. e-mail: pgonzalez@correo.cua.uam.mx.

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