When awaiting 'Bio' Champollion: dynamic programming regularization of the protein secondary structure predictions |
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Authors: | Zimmermann K. |
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Affiliation: | CECAM, Orsay, France Unité d'lngénierie des Protéines, Bâtiment des Biotechnologies, INRA, 78352 Jouy-en-Josas, France |
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Abstract: | Predictions of protein secondary structure using current methodsare often unrealistic, i.e. the predicted -helices or ß-strandsare too short. To improve the realism, various heuristic filteringor smoothing methods are used. They are more orless intuitive and are based on ad hoc corrections. We presenta regularization method to obtain a realistic secondary structurefrom predicted propensities. It is based on the known dynamicprogramming algorithm and is quite objective. It can be usedwith any prediction method which yields propensities. The regularizedpredictions conserve well the overall prediction accuracy andimprove the protein-likeness of the prediction. |
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Keywords: | dynamic programming/ filtering/ morphological constraints/ protein secondary structure prediction/ realism/ regularization |
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