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Open Access Research article

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

Marc N Offman, Alexander L Tournier and Paul A Bates*

Author Affiliations

Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, London, WC2A 3PX, UK

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BMC Structural Biology 2008, 8:34  doi:10.1186/1472-6807-8-34

Published: 1 August 2008

Abstract

Background

Automatic protein modelling pipelines are becoming ever more accurate; this has come hand in hand with an increasingly complicated interplay between all components involved. Nevertheless, there are still potential improvements to be made in template selection, refinement and protein model selection.

Results

In the context of an automatic modelling pipeline, we analysed each step separately, revealing several non-intuitive trends and explored a new strategy for protein conformation sampling using Genetic Algorithms (GA). We apply the concept of alternating evolutionary pressure (AEP), i.e. intermediate rounds within the GA runs where unrestrained, linear growth of the model populations is allowed.

Conclusion

This approach improves the overall performance of the GA by allowing models to overcome local energy barriers. AEP enabled the selection of the best models in 40% of all targets; compared to 25% for a normal GA.