General
This is PDB-REDO web server. Before using it, please read the privacy policy.
This is PDB-REDO web server. Before using it, please read the privacy policy.
There are two main references for PDB-REDO depending on whether you refer to the server or the databank.
| Web server | Joosten RP, Long F, Murshudov GN, Perrakis A. The PDB_REDO server for macromolecular structure model optimization. IUCrJ. 2014; 1(4):213-220. |
| Databank | 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. |
Below are other publications that describe different algorithms and concepts of PDB-REDO.
| No data, no PDB‑REDO | 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. |
| The first PDB-REDO | 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. |
| 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. |
| 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. |
| Loop building | van Beusekom B, Joosten K, Hekkelman ML, Joosten RP, Perrakis A. Homology-based loop modeling yields more complete crystallographic protein structures. IUCrJ 2018; 5:585-594. |
| N-glycan building | van Beusekom B, Wezel N, Hekkelman ML, Perrakis A, Emsley E, Joosten RP. Building and rebuilding N-glycans in protein structure models. Acta Cryst. 2019; D75:416-425. |
| Nucleic acids | de Vries I, Kwakman T, Lu X-J, Hekkelman ML, Deshpande M, Velankar S, Perrakis A, Joosten RP. New restraints and validation approaches for nucleic acid structures in PDB-REDO. Acta Cryst. 2021; D77:1127-1141. |
| Zinc sites | Touw WG, van Beusekom B, Evers JMG, Vriend G, Joosten RP. Validation and correction of Zn–CysxHisy complexes. Acta Cryst. 2016; D72:1110-1118. |