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The Protein Structure Discovery system is designed for the annotation of the function-structure of protein, its immunological properties, polymorphisms, its involvement in metabolic pathways, and for phylogenetic analysis.

Protein functional annotation involves search for homologs in protein annotated sequence databases, gene ontology protein function identification, prediction of gene expression level, protein functional site recognition, prediction of protein subcellular localization, and analysis of protein structure-activity relationships.

Structure annotation involves prediction of protein tertiary structure by homology modeling and identification of structural homologs in the PDB database using structural alignment.

For polymorphism analysis, the database for human gene and protein polymorphisms, programs for prediction of mutation effect on protein thermodynamic stability and functional sites, also prediction of mutant protein activity are implemented.

Analysis of protein immunological properties involves prediction of B-epitopes and sites of constitutive and immunoproteosomal proteolysis.

Protein phylogenetic analysis involves multiple sequence alignment, protein phylogenetic tree reconstruction, and correlation analysis of amino acid substitutions.

The involvement of a particular protein in metabolic pathways was established using the Associative Network Discovery (AND©) system that allows to reconstruct metabolic pathways from the KEGG database.