An Ecologically-Inspired Parallel Approach Applied To The Protein Structure Reconstruction From Contact Maps

The Protein Folding Problem (PFP) is considered one of the most important open challenges in Biology and Bioinformatics. This paper describes the application of a parallel ecology-inspired algorithm (pECO) to a hard problem related to the PFP: the protein structure reconstruction from Contact Maps. The fitness function proposed includes information not only about the free-energy of the conformation, but also similarity measures commonly used in classification systems. Experiments were done to evaluate the adequacy of the proposed approach. Results show that the combination of concurrent evolutionary approaches take advantage of both the coevolution effect and the different search strategies. Furthermore, it is observed that parallel processing was not only justified but also essential for obtaining results in reasonable processing time.