Remote-3DD: a new remote homology detection method that uses physicochemical properties
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In this paper, we present a new method for remote homology detection called remote-3DD. The proposed method combines predicted contact maps and distributions of the interaction matrices. Predicted contact maps approximate the 3D shape of a protein based on its primary structure. On the other hand, an interaction matrix allows representing a protein by using the physicochemical properties of its amino acids. The remote-3DD method is proposed as a strategy to improve the accuracy of the remote-C3D method, which uses contact maps alone. In this paper, we hypothesize that we can improve the accuracy of the remote-C3D method by including physicochemical properties. The results show that the accuracy of the remote-3DD method is higher than the accuracy of the composition-based methods and in some cases comparable with the accuracy of the profile-based methods. In addition, the results also show that the remote-3DD method achieves higher accuracy values than the remote-C3D method when considering the same number of models and size of submatrices.
- Oscar F. Bedoya, Irene Tischer, Remote homology detection of proteins using 3D models enriched with physicochemical properties , Ingeniería y Competitividad: Vol. 17 No. 1 (2015): Revista Ingeniería y Competitividad
- Claudia X. Mazo, Oscar F. Bedoya, PESPAD: a new tool for protein secondary structure prediction based on decision trees. , Ingeniería y Competitividad: Vol. 12 No. 2 (2010)
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