Accepted:
00/00/1994
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/vol01/fullen01/ | © Copyright 1994 | |||
| Volume 1 | Received: Accepted: |
00/00/1994 00/00/1994 |
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Genetic algorithms and recursive ensemble mutagenesis in protein engineering
Füllen, G. & Youvan, D. C. |
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| Abstract | |
| We compare Genetic Algorithms (GAs) and an existing protein engineering method called Recursive Ensemble Mutagenesis (REM), which has proven highly effective both in experimental work and computer simulations. REM tries to find a set of "optimal" amino acids at preselected positions in a given protein so that its functional behavior can be enhanced or altered appropriately. REM utilizes the relationship between genotype (DNA) and phenotype (protein). After a heuristic or experimental evaluation of the fitness of proteins coded by a random initial DNA population, REM calculates a new set of fit DNA sequences, exploiting properties of the genetic code. Moreover, as it would be impractical to resynthesize every single DNA sequence which coded a fit protein, generalized schemata (formae) are calculated that serve as a partially wild-card input for the DNA synthesizer producing the new generation. This procedure has an effect similar to uniform crossover, but it also introduces completely new amino acid residues with related fitness. Although developed independently, REM may be seen as a GA constrained by experimental requirements. However, these constraints give rise to a powerful new optimization and diversification component not found in traditional GAs. | |
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Multimedia Links (none) Reference Links (none) Citation Reference Füllen, G. & Youvan, D. C. (1994), Genetic algorithms and recursive ensemble mutagenesis in protein engineering, Complexity International, Volume 1, Paper ID: fullen01, URL: http://www.complexity.org.au/vol01/fullen01/ |
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