The Netherlands Cancer Institute
NWO logo
Johnson and Johnson logo
West-Life logo
iNEXT logo
Powered by
CCP4 logo
WHAT-IF logo
SDSC logo
3DNA logo
PDB-REDO: updated and optimised crystallographic structures

PDB-REDO is a procedure to optimise crystallographic structure models, providing algorithms that make a fully automated decision making system for refinement, rebuilding and validation. It combines popular crystallographic software from CCP4, e.g. REFMAC and COOT, with with our specially developed rebuilding tools Centrifuge, Pepflip & SideAide and structure analysis tools like WHAT IF and PDB-care. PDB-REDO optimises refinement settings (e.g. geometric and B-factor restraint weights, B-factor model, TLS groups, NCS and homology restraints), refines with REFMAC, partially rebuilds the structure (rejects waters, refines side chains, checks peptide planes), refines some more, and then validates the results.

With PDB-REDO you can obtain updated and optimised versions of existing entries of the PDB from our DataBank, or you can optimise your own structure model using our Server. If you want to know more or install PDB-REDO on your own computers, please check below.

PDB-REDO Databank

The PDB-REDO databank contains optimised versions of existing PDB entries with electron density maps, a description of model changes, and a wealth of model validation data. It is a good starting point for any structural biology project.

All the entries are treated with a consistent protocol that reduces the effects of differences in age, software, and depositors. This makes PDB-REDO a great datatset for large scale structure analysis studies.

Here you can find more information about downloading PDB-REDO databank entries. And here you can find the data usage license.

PDB-REDO server

The PDB-REDO server helps you to get a publication quality structure. It takes your current model (PDB), diffraction data (MTZ), and (optional) ligand restraints and it returns a new model, new maps, validation reports, and many tools to continue working on your model, including COOT menus customised for inspecting your structure.

Click on the links below to download the software, access the PDB-REDO databank, etc

PDB-REDO software Download the scripts and programs (Linux and Bash on Windows 10)
REFMAC The PDB-REDO refinement engine from the G. Murshudov group

The Science behind PDB-REDO

Click on the links below to get a reprint of PDB-REDO publications

Web server Joosten RP, Long F, Murshudov GN, Perrakis A. The PDB_REDO server for macromolecular structure model optimization. IUCrJ. 2014 May 30;1(Pt 4):213-20.
Decision making Joosten RP, Joosten K, Murshudov GN, Perrakis A. PDB_REDO: constructive validation, more than just looking for errors. Acta Cryst. 2012; D68:484-496.
Model rebuilding Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A. Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank. Bioinformatics 2011; 27:3392-3398.
Database stuff Joosten RP, Te Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, Vriend G. A series of PDB related databases for everyday needs. Nucl. Acids Res. 2011; 39:D411-D419.
No data, no re‑refinement Joosten RP, Vriend G. PDB improvement starts with data deposition. Science 2007; 317:195-196.
The value of re‑refinement Joosten RP, Womack T, Vriend G, Bricogne G. Re-refinement from deposited X‑ray data can deliver improved models for most PDB entries. Acta Cryst. 2009; D65:176-185.
PDB-REDO idea Joosten RP, et al and Vriend G. PDB_REDO: automated re‑refinement of X‑ray structure models in the PDB. J. Appl. Cryst. 2009; 42:376-384.
Homology restraints van Beusekom B, Touw WG, Tatineni M, Somani S, Rajagopal G, Luo J, Gilliland GL, Perrakis A, Joosten RP Homology-based hydrogen bond information improves crystallographic structures in the PDB. Protein Science. 2018;27:798-808.