Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.

Abstract

AVAILABILITY AND IMPLEMENTATION

The PDB_REDO database and links to all software are available at http://www.cmbi.ru.nl/pdb_redo.

MOTIVATION

Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users.

CONTACT

r.joosten@nki.nl; a.perrakis@nki.nl

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

RESULTS

We developed new algorithms to allow automatic rebuilding and remodeling of main chain peptide bonds and side chains in crystallographic electron density maps, and incorporated these and further enhancements in the PDB_REDO procedure. Applying the updated PDB_REDO to the oldest, but also to some of the newest models in the PDB, corrects existing modeling errors and brings these models to a higher quality, as judged by standard validation methods.