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1.  Comment on Timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013) 
A response to the article by Joosten et al. [(2013), Acta Cryst. D69, 2293–2295].
The wwPDB responds to the article by Joosten et al. [(2013), Acta Cryst. D69, 2293–2295].
PMCID: PMC3852647  PMID: 24311570
wwPDB; deposition; macromolecular data
2.  Comment on On the propagation of errors by Jaskolski (2013) 
A response to the article by Jaskolski [(2013), Acta Cryst. D69, 1865–1866].
The wwPDB responds to the article by Jaskolski [(2013), Acta Cryst. D69, 1865–1866].
PMCID: PMC3852648  PMID: 24311571
wwPDB; errors; 
3.  Implementing an X-ray validation pipeline for the Protein Data Bank 
The implementation of a validation pipeline, based on community recommendations, for future depositions of X-ray crystal structures in the Protein Data Bank is described.
There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate all of the entries already in the PDB as well as all structures that will be deposited in the future. The recommendations of the X-ray VTF are currently being implemented in a software pipeline. Here, ongoing work on this pipeline is briefly described as well as ways in which validation-related information could be presented to users of structural data.
PMCID: PMC3322607  PMID: 22505268
validation; data archives; biomacromolecular structure; PDB
4.  The role of structural bioinformatics resources in the era of integrative structural biology 
The integration of structural data on atomistic to cellular scales with genetic, taxonomic and functional information is discussed. The challenges to the PDB and EMDB archives and some pertinent developments at PDBe to address these are discussed.
The history and the current state of the PDB and EMDB archives is briefly described, as well as some of the challenges that they face. It seems natural that the role of structural biology archives will change from being a pure repository of historic data into becoming an indispensable resource for the wider biomedical community. As part of this transformation, it will be necessary to validate the biomacromolecular structure data and ensure the highest possible quality for the archive holdings, to combine structural data from different spatial scales into a unified resource and to integrate structural data with functional, genetic and taxonomic data as well as other information available in bioinformatics resources. Some recent developments and plans to address these challenges at PDBe are presented.
PMCID: PMC3640467  PMID: 23633580
structural bioinformatics; integrative structural biology; PDBe
5.  The Protein Data Bank in Europe (PDBe): bringing structure to biology 
Some future challenges for the PDB and its guardians are discussed and current and future activities in structural bioinformatics at the Protein Data Bank in Europe (PDBe) are described.
The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described.
PMCID: PMC3069747  PMID: 21460450
Protein Data Bank in Europe
6.  Crystallographic refinement of ligand complexes 
Methods and resources for obtaining chemically plausible starting models and restraint sets for refinement of ligand complexes are described and some of the potential pitfalls are discussed.
Model building and refinement of complexes between biomacromolecules and small molecules requires sensible starting coordinates as well as the specification of restraint sets for all but the most common non-macromolecular entities. Here, it is described why this is necessary, how it can be accomplished and what pitfalls need to be avoided in order to produce chemically plausible models of the low-molecular-weight entities. A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed.
PMCID: PMC2483469  PMID: 17164531
refinement; model building; ligand complexes; restraint sets; macromolecular crystallography

Results 1-6 (6)