MOIRAE: A computational strategy to extract and represent structural information from experimental protein templates

The prediction and analysis of the three- dimensional (3D) structure of proteins is a key research problem in Structural Bioinformatics. The 1990's Genome Projects resulted in a large increase in the number of available protein sequences. However, the number of identified 3D protein structures have not followed the same growth trend. Currently, the number of available protein sequences greatly exceeds the number of known 3D structures. Many computational methodologies, systems and algorithms have been proposed to address the protein structure prediction problem. However, the problem still remains challenging because of the complexity and high dimensionality of a protein conformational search space. The most significant progress in the last Critical Assessment of protein Structure Prediction was achieved by methods that use database information. Nevertheless, a major challenge remains in the development of better strategies for template identification and representation. This article describes a computational strategy to acquire and represent structural information of experimentally determined 3D protein structures. A clustering strategy was combined with artificial neural networks in order to extract structural information from experimental protein structure templates. In the proposed strategy, the main efforts focus on the acquisition of useful and accurate structural information from 3D protein templates stored in the Protein Data Bank (PDB). The proposed method was tested in twenty protein sequences whose sizes vary from 14 to 70 amino acid residues. Our results show that the proposed method is a good way to extract and represent valuable information obtained from the PDB and also significantly reduce the 3D protein conformational search space.