Structural Biochemistry/Bioinformatics/Structural Alignments/Programs Used For Structural Alignment/TOPOFIT

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The TOPOFIT method analyzes protein structures using three-dimensional Delaunay triangulation patterns derived from backbone representation. Structural related proteins have been found to have a common spatial invariant part, a set of tetrahedrons, mathematically described as a common spatial sub-graph volume of the three-dimensional contact graph derived from Delaunay tessellation (DT). Due to this property of protein structures, a novel common volume superimposition (TOPOFIT) method is presented to produce structural alignments of proteins. The superimposition of the DT patterns allows the common number of equivalent residues to be objectively identified. In other words, TOPOFIT identifies a feature point on the RMSD/Ne curve, a topomax point, until which two structures correspond to each other including backbone and inter-residue contacts, while the growing number of mismatches between the DT patterns occurs at larger RMSD (Ne) after the topomax point. The topomax point is present in all alignments from different protein structural classes. Therefore, the TOPOFIT method identifies common, invariant structural parts between proteins. The TOPOFIT method introduces new opportunities for the comparative analysis of protein structures and for more detailed studies on understanding the molecular principles of tertiary structure organization and functionality. This helps to detect conformational changes, topological differences in variable parts, which are particularly important for studies of variations in active/binding sites and protein classification.