Brian D. Cloteaux and Nadezhda Serova
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Protein structure, alpha helix placement
Because of the complexity in determining the 3D structure of a protein, the use of partial information determined from experimental techniques can greatly reduce the overall computational expense. We investigate the problem of matching experimentally observed lengths of helices to the predicted secondary structure of a protein. We give a simple and fast algorithm for producing a library of potential solutions. We test our algorithm by performing a series of computational experiments for predicting the alpha helix placement of proteins with an already known order. These tests seem to demonstrate that our method, if given a good prediction of the protein’s secondary structure, can generate high quality lists of potential placements of the helix lengths onto the protein sequence.