Abstract
The determination of the three-dimensional structure of a protein is one of the most challenging problems of modern science. A genetic algorithm (GA) was developed to find low energy conformations under an atomist protein model. A crowding method was used for parental replacement. The comparison criterion between individuals was the absolute RMSD of the C β positions’ of the residues. The GROMOS96 force field potential energy function was used to evaluate the energy of the conformations. We tested the performance of the GA against poly-alanine sequences of lengths 18 and 23 in a situation where the global minimum was an alpha helix, and also when it was some other compact structure. The GA proved very efficient by having a 100% success ratio in finding both the global minimum and the alpha helix conformation in all situations.
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Custódio, F.L., Barbosa, H.J.C., Dardenne, L.E. (2007). Genetic Algorithm for Finding Multiple Low Energy Conformations of Poly Alanine Sequences Under an Atomistic Protein Model. In: Sagot, MF., Walter, M.E.M.T. (eds) Advances in Bioinformatics and Computational Biology. BSB 2007. Lecture Notes in Computer Science(), vol 4643. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73731-5_17
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DOI: https://doi.org/10.1007/978-3-540-73731-5_17
Publisher Name: Springer, Berlin, Heidelberg
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