PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Sammanfattning

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

Publicerad i

Journal of Applied Crystallography
2009, volym: 42, nummer: 3, sidor: 376-384

SLU författare

• Bongcam Rudloff, Erik

  • Uppsala universitet

UKÄ forskningsämne

Bioinformatik (beräkningsbiologi)

Publikationens identifierare

• DOI: https://doi.org/10.1107/S0021889809008784

Permanent länk till denna sida (URI)

https://res.slu.se/id/publ/27187