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A method of predicting the secondary protein structure based on dictionaries

Roterman-Konieczna I., Fabian P., Stąpór K.

Bio-Algorithms and Med-Systems

2015

Vol. 11, no. 3

163--170

The shape of a protein chain may be analyzed at different levels of details. The ultimate shape description contains three-dimensional coordinates of all atoms in the chain. In many cases, a description of the local shape, namely secondary structure, is enough to determine some properties of proteins. Although obtaining the full threedimensional (3D) information also defines the secondary structure, the problem of finding this precise 3D shape (tertiary structure) given only the amino acid sequence is very complex. However, the secondary structure may be found even without having the full 3D information. Many methods have been developed for this purpose. Most of them are based on similarities of the analyzed protein chain to other proteins that are already analyzed and have a known secondary structure. The presented paper proposes a method based on dictionaries of known structures for predicting the secondary structure from either the primary structure or the so-called structural code. Accuracies of up to 79% have been achieved.