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Multi-agent simulation of protein folding (2005)
| Venue: | In Proceedings of MAS-BIOMED 2005 |
| Citations: | 3 - 2 self |
BibTeX
@INPROCEEDINGS{Bortolussi05multi-agentsimulation,
author = {Luca Bortolussi and Agostino Dovier and Federico Fogolari},
title = {Multi-agent simulation of protein folding},
booktitle = {In Proceedings of MAS-BIOMED 2005},
year = {2005}
}
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Abstract
Abstract. A protein is identified by a finite sequence of amino acids, each of them chosen from a set of 20 elements. The Protein Structure Prediction Problem, fundamental for biological and pharmaceutical research, is the problem of predicting the 3D native conformation of a protein, when its sequence of amino acids is known. All current mathematical models of the problem are affected by intrinsic computational limits, and by a disagreement on which is the most reliable energy function to be used. In this paper we present an agent-based framework for ab-initio simulations, composed by different levels of agents. Each amino acid of an input protein is viewed as an independent agent that communicates with the others. These agents are coordinated by strategic and cooperative higher level agents. The framework allows a modular representation of the problem and it is easily extensible for further refinements and for different energy functions. Simulations at this level of abstraction allow fast calculation, distributed on each agent. We provide an implementation using the Linda package of SICStus Prolog, to show the feasibility and the power of the method.
Keyphrases
amino acid protein folding multi-agent simulation linda package different energy function current mathematical model ab-initio simulation level agent finite sequence sicstus prolog input protein pharmaceutical research reliable energy function modular representation intrinsic computational limit independent agent different level fast calculation protein structure prediction problem native conformation agent-based framework
