Fastprot: A Computational Workbench for Recognition of the Structural and Functional Determinants in Protein Tertiary Structures

The recognition of the structural/functional determinants in proteins has broad implications for structural and functional genomics. A better understanding of these determinants, such as protein-protein, protein-DNA, and protein-RNA interaction sites, would provide insight into protein functions. A computational workbench for the recognition of functional sites in protein tertiary structure combined with molecular complex reconstruction, estimation of mutation effect on protein thermodynamic stability, as well as search for the structure-activity relationships in homologous protein set was developed. Here, we illustrate the capabilities of the workbench by providing examples of (1) search for interactions of the hepatitis C virus proteins with the human proteins, (2) analysis of the potential toxicity of molecular compounds, (3) analysis of structure-activity relationships in the disintegrin family, and (4) structural protein classification based on the structural similarity to the functional sites.