Niche Genetic Algorithms are better than traditional Genetic Algorithms for Protein Folding

Here we demonstrate that Niche Genetic Algorithms (NGA) are better at computing protein folding than traditional Genetic Algorithms (GA). de novo Previous research has shown that proteins can fold into their active forms in a limited number of ways; however, predicting how a set of amino acids will fold starting from the primary structure is still a mystery. GAs have a unique ability to solve these types of scientific problems because of their computational efficiency. Unfortunately, GAs are generally quite poor at solving problems with multiple optima. However, there is a special group of GAs called Niche Genetic Algorithms (NGA) that are quite good at solving problems with multiple optima. In this study, we use a specific NGA: the Dynamic-radius Species-conserving Genetic Algorithm (DSGA), and show that DSGA is very adept at predicting the folded state of proteins, and that DSGA is better than a traditional GA in deriving the correct folding pattern of a protein. James A. Coker ( ) Corresponding author: [email protected] Brown MS, Bennett T and Coker JA. How to cite this article: Niche Genetic Algorithms are better than traditional Genetic Algorithms for 2014, :236 (doi: ) Protein Folding [version 1; referees: 2 not approved] de novo F1000Research 3 10.12688/f1000research.5412.1 © 2014 Brown MS . This is an open access article distributed under the terms of the , which Copyright: et al Creative Commons Attribution Licence permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the (CC0 1.0 Public domain dedication). Creative Commons Zero "No rights reserved" data waiver The author(s) declared that no grants were involved in supporting this work. Grant information: Competing interests: No competing interests were disclosed. 07 Oct 2014, :236 (doi: ) First published: 3 10.12688/f1000research.5412.1 Referee Status: