PDB-REDO databank of optimised macromolecular structures
PDB-REDO databank of optimised macromolecular structures refines and rebuilds macromolecular models from the Protein Data Bank to improve structural quality and fit to crystallographic experimental data.
Key Features:
- Systematic refinement and rebuilding: Applies automated rebuilds and optimization rounds to improve model geometry and agreement with experimental data.
- Decision-making framework: Integrates existing and custom-built software modules to select optimal refinement protocols.
- B-factor and TLS adjustments: Performs anisotropic or isotropic B-factor refinement and TLS model adjustments as selected by the framework.
- Side-chain and peptide-plane rebuilding: Automatically rebuilds side chains and peptide planes to correct local modeling errors.
- Improvement metrics: Targets reductions in R(free) and improvements in geometric validation metrics.
- Main-chain rebuilding from density: Uses algorithms to rebuild main-chain peptide bonds and side chains from electron density maps.
- Zinc ion complex handling: Validates and corrects geometric distortions in tetrahedral zinc complexes with cysteine and histidine ligands and refines validation targets using observed trends.
- N-glycosylation handling: Automatically rebuilds or extends carbohydrate residues within N-glycosylation trees.
Scientific Applications:
- Structural model improvement: Improves structural quality of PDB entries by correcting modeling errors and enhancing fit to experimental crystallographic data.
- Metal-binding site refinement: Refines geometry and validation of zinc-binding sites involving cysteine and histidine ligands.
- Carbohydrate modelling: Rebuilds and extends glycosylation trees to improve carbohydrate representation in macromolecular structures.
- Databank of optimised structures: Produces an updated set of optimized PDB models for downstream structural biology, modelling, and validation studies.
- Benchmarking: Demonstrated improvements across over 12,000 PDB entries during validation and testing.
Methodology:
Integrates existing and custom software modules within a decision-making framework to select anisotropic or isotropic B-factor refinement and TLS adjustments, performs automatic rebuilding of main-chain peptide bonds and side chains from electron density maps, validates and corrects tetrahedral zinc complexes with cysteine and histidine ligands using observed trends to refine validation targets, and automatically rebuilds or extends carbohydrate residues in N-glycosylation trees.
Topics
Collections
Details
- License:
- Freeware
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 10/7/2015
- 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.
van Beusekom B, Joosten K, Hekkelman ML, Joosten RP, Perrakis A. Homology-based loop modeling yields more complete crystallographic protein structures. IUCrJ. 2018;5(5):585-594. doi:10.1107/s2052252518010552. PMID:30224962. PMCID:PMC6126648.
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.
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.
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 <scp>PDB</scp>. Protein Science. 2017;27(3):798-808. doi:10.1002/pro.3353. PMID:29168245. PMCID:PMC5818736.
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.
Touw WG, Joosten RP, Vriend G. New Biological Insights from Better Structure Models. Journal of Molecular Biology. 2016;428(6):1375-1393. doi:10.1016/j.jmb.2016.02.002. PMID:26869101.
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.
van Beusekom B, Wezel N, Hekkelman ML, Perrakis A, Emsley P, Joosten RP. Building and rebuilding N-glycans in protein structure models. Acta Crystallographica Section D Structural Biology. 2019;75(4):416-425. doi:10.1107/s2059798319003875. PMID:30988258. PMCID:PMC6465985.
Documentation
Downloads
- Downloads pagehttps://pdb-redo.eu/download-info.html