PDB-REDO databank
PDB-REDO databank refines protein structure models from the Protein Data Bank (PDB) using automated re-refinement and rebuilding to improve fit to experimental X-ray data and geometric quality for downstream structural analyses.
Key Features:
- Automated Re-refinement: Improves fit to experimental X-ray data and enhances geometric quality using automated protocols including Translation/Libration/Screw (TLS) models to account for concerted atom movements.
- Advanced Algorithms: Performs automatic rebuilding and remodeling of main-chain peptide bonds and side chains guided by crystallographic electron density maps.
- Validation and Correction: Validates and corrects common structural anomalies such as geometrically distorted zinc complexes in tetrahedral coordination with cysteine and histidine ligands.
- Comprehensive Validation Data: Produces validation data that detail model quality metrics and the changes made relative to the original PDB entries.
- Large-Scale Consistency: Applies consistent treatment across structural models to improve their suitability for large-scale analyses and data mining.
Scientific Applications:
- Teaching protein structure: Provides refined models for teaching protein structure principles and geometry.
- Ligand optimization in drug development: Improves the accuracy of protein–ligand coordinates used for ligand optimization in drug development.
- Homology modeling: Supplies higher-quality templates to improve homology modeling outcomes.
- Rational drug design: Enables structure-based rational drug design by providing improved three-dimensional coordinates.
- Structural biology and large-scale analyses: Facilitates structural biology studies and large-scale comparative analyses that require uniform, validated model sets.
Methodology:
Uses large-scale benchmarking of thousands of PDB entries, automated re-refinement and rebuilding (including TLS models), and grid computing to manage the computational demands.
Topics
Details
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 10/30/2016
- Last Updated:
- 11/24/2024
Operations
Publications
Joosten RP, Womack T, Vriend G, Bricogne G. Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. Acta Crystallographica Section D Biological Crystallography. 2009;65(2):176-185. doi:10.1107/s0907444908037591. PMID:19171973. PMCID:PMC2631631.
Joosten RP, Joosten K, Murshudov GN, Perrakis A. <i>PDB_REDO</i>: constructive validation, more than just looking for errors. Acta Crystallographica Section D Biological Crystallography. 2012;68(4):484-496. doi:10.1107/s0907444911054515. PMID:22505269. PMCID:PMC3322608.
van Beusekom B, Perrakis A, Joosten RP. Data Mining of Macromolecular Structures. Methods in Molecular Biology. 2016. doi:10.1007/978-1-4939-3572-7_6. PMID:27115630.
Joosten RP, Vriend G. PDB Improvement Starts with Data Deposition. Science. 2007;317(5835):195-196. doi:10.1126/science.317.5835.195. PMID:17626865.
Touw WG, Baakman C, Black J, te Beek TAH, Krieger E, Joosten RP, Vriend G. A series of PDB-related databanks for everyday needs. Nucleic Acids Research. 2014;43(D1):D364-D368. doi:10.1093/nar/gku1028. PMID:25352545. PMCID:PMC4383885.
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. Nucleic Acids Research. 2010;39(Database):D411-D419. doi:10.1093/nar/gkq1105. PMID:21071423. PMCID:PMC3013697.
Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund A, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G. PDB_REDO: automated re-refinement of X-ray structure models in the PDB. Journal of Applied Crystallography. 2009;42(3):376-384. doi:10.1107/s0021889809008784. PMID:22477769. PMCID:PMC3246819.
Touw WG, van Beusekom B, Evers JMG, Vriend G, Joosten RP. Validation and correction of Zn–Cys <i> <sub>x</sub> </i> His <i> <sub>y</sub> </i> complexes. Acta Crystallographica Section D Structural Biology. 2016;72(10):1110-1118. doi:10.1107/s2059798316013036. PMID:27710932. PMCID:PMC5053137.
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(24):3392-3398. doi:10.1093/bioinformatics/btr590. PMID:22034521. PMCID:PMC3232375.