Native Protein Data Bank and Gallery of Protein Structure Animations

The Gallery of 3D Native Protein Structures has been renamed "Native Protein Data Bank and Gallery of Protein Structure Animations" because it includes the facility to download full structural coordinates of native proteins and because it is expected the collection will grow. The reliability of most of these structures is now known to be very high. For barrel structures, the practice of pointing the barrels towards the origin and docking them symmetrically can be shown to produce structures with very high statistical correlation with other features and functions. For the viral neuraminadases, the appropriate locations of glycosylation sites, each with a probability of appropriate location by chance of about 2 in 3, taken together amount to a probability by chance of less than 1 in a thousand. For the hemoglobins of mammals, crocodiles, rays and sharks, the appropriate locations of allosteric binding sites and a variation in structure coordinated between alpha and beta chains, the combined probability of happening by chance is again about 1 in a thousand. Both these groups of protein structures were achieved by the same pointing and docking procedure and so we can say that the probability of this procedure producing meaningful structures by chance is about 1 in a million. As successful examples accumulate, while unsuccessful examples are rare, it seems that the statistical significance will continue to rise. Users of the Gallery part of the site will now find it easier to use as I have obtained a Symantec/Verisign Code Signing certificate. This allows Java to run the Jmol molecular viewer with only one request for permission from the user.