BORGES a program to retrieve local polypeptide folds and phase crystallographic structures at 2Å enforcing tertiary structure

Any unknown structure should contain fragments already seen in the PDB, but how to retrieve and exploit this information?
The PDB database contains a vast amount of information and for any unknown structure, given small enough fragments (e.g. two helices or three strands in a particular disposition), similar models (<0.5Å rmsd) are bound to occur in some of the deposited entries. In analogy to Borges’ “Library of Babel” that enclosed books with all random combinations of letters and therefore held any possible book, the information required to phase a structure through fragment search and density modification should already be present somewhere in the PDB. The more so as unlike “Borges library”, the PDB is non-random, containing in all sort of structural contexts only meaningful structural units. In addition, to bootstrap phasing our method requires small sentences instead of complete volumes, that is, a small fraction of perfect mainchain rather than a complete description of the structure.


The Librarian (1566).
Giuseppe Arcimboldo.

Exploiting tertiary structure through local folds for crystallographic phasing Massimo Sammito, Claudia Millán, Dayté D. Rodríguez, Iñaki M. de Ilarduya, Kathrin Meindl, Ivan De Marino, Giovanna Petrillo, Rubén M. Buey, José M. de Pereda, Kornelius Zeth, George M. Sheldrick and Isabel Usón.

Nature Methods 10: 1099-1101 (2013) (doi:10.1038/nmeth.2644)