Home Pairwise comparison One-2-All search TOPOFIT-database Interface Software (Friend) Contact Us TOPOFIT-DB, a comprehensive database of accurate protein structure alignments by TOPOFIT

Navigation Menu Topofit Home T-Pair Pairwise Comparison One-2-All Search TOPOFIT-database T-DB with SCOP IDs T-DB with CATH IDs Interface Software Statistics Examples Help Contact Us Examples ... View of superimposed residues in active sites of two endonucleases (PDB-codes ‘1fiu’ chain A and ‘1cfr’) which share 13% of the sequence identity. The structure ‘1fiu’ is in green and ‘1cfr’ is in violet. Residues are shown in “ball&stick” mode. The distances between atoms in corresponding active site residues are less than 1 Å. The overall superposition has 113 points with RMSD of 1.6 Å and Z-Score of 7.9 Structural alignment of two lipocalins (PDB-code ‘1ngl’ chain A and ‘1beb’ chain A) which share only 17% sequence identity. Common parts used in superimposition are displayed in bold. The TOPOFIT finds structural core of the two proteins. The superimposition has 97 points with RMSD of 1.7 Å and Z-Score of 5.7

TOPOFIT-DB web link: topofit.ilyinlab.org TOPOFIT-DB Reference: Chesley M.Leslin, Alexej Abyzov, and Valentin A. Ilyin, TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Research 2007 35(Database issue):D317-D321 TOPOFIT Reference: Valentin A. Ilyin, Alexej Abyzov, and Chesley M.Leslin, Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Science (2004), 13:1865-1874.         Sunday 05th 2012f February 2012 06:02:21 AM