D2CHECK

This web site, called D2CheckServer automates the process for obtaining D 2 Check values. Given a PDB ID or user-provided PDB file, it calculates and displays the associated &Phi - &Psi (i.e. Ramachandran) and &Psi i-&Phi i+1 plots. Using this information the server proceeds to calculate the D 2 Check value and the results are presented in two complementary forms. First, the D 2 Check value averaged over the entire protein is displayed with respect to the distribution of all proteins sampled in the PDB. The value is defined such that it simply represents the standard deviation from the mean of the distribution of proteins in the PDB. Therefore, larger D 2 Check values indicate that a given protein is increasingly dissimilar to the ensemble of structures in the PDB. To further aid in the analysis, a more detailed representation that assigns D 2 Check values at the residue level are also presented in the form of a convenient color strip. In this manner, it becomes easy to locate..