2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content

Abstract

Abstract 2StrucCompare is a webserver whose primary aim is to visualize subtle but functionally important differences between two related protein structures, either of the same protein or related homologues, with similar or functionally different tertiary structures. At the heart of the package is identifying and visualizing differences between conformations at the secondary structure and at the residue level, such as contact differences or side chain conformational differences found between two protein chains. The protein secondary structures are determined according to four established methods (DSSP, STRIDE, P-SEA and STICKS), and as each employs different assignment strategies, small conformational differences between the two structures can give rise to paired residues being denoted as having different secondary structure features with the different methods. 2StrucCompare captures both the large and more subtle differences found between structures, enabling visualization of these differences that could be key to an understanding of a proteins’ function. 2StrucCompare is freely accessible at http://2struccompare.cryst.bbk.ac.uk/index.php