25 YEARS OF THE PDB: IMPACT ON STRUCTURAL BIOLOGY. David R. Davies, Gerson H. Cohen, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda MD 20892

The current explosive expansion of structural biology has profited greatly from the existence of the PDB. In methodology, ready access to coordinates has facilitated the development and application of phase determining procedures such as molecular replacement. Analysis of the PDB has also provided statistical criteria for structural evaluation.

However, it is the area of comparative protein structure analysis that has been most affected by the flood of new structures and the availability of coordinates. Although many protein superfamilies (eg immunoglobulins, serine proteases etc) are related by similar functional properties and by sequence homologies, others (TIM barrels, 4 alpha helix bundles) are not and structural analysis has revealed hitherto unsuspected relations between proteins that are unsupported by functional or sequence similarities. Sophisticated procedures have been developed to analyse the relatedness of members of these families. As the number of protein entries in the PDB continues to rise, estimates can be made of the total number of independent protein folds which appears to be finite. A continuing goal will be to provide a basis for protein structure prediction based on amino acid sequence.

Blundell T. L. and Johnson M. S. Protein Science, 1993, 2:877

Murzin A. G., Brenner S. E., Hubbard T. and Chothia C. J Mol Biol, 1995, 247:536

Orengo C. A., Flores T. P., Taylor W. R. and Thornton J. M. Protein Engineering, 1993, 6:485.