PT  - JOURNAL ARTICLE
AU  - Bart van Beusekom
AU  - Wouter G. Touw
AU  - Mahidhar Tatineni
AU  - Sandeep Somani
AU  - Gunaretnam Rajagopal
AU  - Jinquan Luo
AU  - Gary L. Gilliland
AU  - Anastassis Perrakis
AU  - Robbie P. Joosten
TI  - Homology-based hydrogen bond information improves crystallographic structures in the PDB
AID  - 10.1101/147231
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 147231
4099  - http://biorxiv.org/content/early/2017/06/21/147231.short
4100  - http://biorxiv.org/content/early/2017/06/21/147231.full
AB  - Crystallographic structure models in the Protein Data Bank (PDB) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures, especially at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. Using approximately 60 years of CPU-time in massively parallel computing, we constructed a new instance of the PDB-REDO databank, a novel resource to help biologists gain insight on protein families or on specific structures, as we demonstrate with examples.