Comparative Analysis of Different Methods for the Detection of Specificity Regions in Protein Families

摘要

Many proteins have evolved to form specific molecular complexes and the specificity of this interaction is essential for their function. Molecular interactions are likely to impose constrains on protein sequences around the regions of binding. At molecular level these regions can be detected by the presence of evolutionary conserved but chemically different aminoacids between related proteins of different function. The-oretical methods for the identification of these regions could be of great interest in combination with direct experimental approaches. Here we compare different methods for the detection of the residues integrating these regions (tree-determinant residues). Three of these methods have already been published and a fourth one, based on a Self-Organizing Map algorithm is introduced here. The methods are tested in two different families: alpha subunit of trimeric G-proteins and Drosophila short-chain Alcohol Dehydrogenase.