PDBe: Protein Data Bank in Europe

By S. Velankar, Younes Alhroub, Anaëlle Alili, Christoph Best, Harry Boutselakis, S. Caboche, M. J. Conroy, J. M. Dana, G. V. Ginkel, Adel Golovin and 23 more. 2010

289 citations recorded by the source corpus.

The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; wwpdb.org). PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community. PDBe has developed a browser to access and analyze the structural archive using classification systems that are familiar to chemists and biologists. The PDBe web pages that describe individual PDB entries have been enhanced through the introduction of plain-English summary pages and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures determined by means of NMR spectroscopy has been expanded. Finally, the entire web site has been redesigned to make it substantially easier to use for expert and novice users alike. PDBe works closely with other teams at the European Bioinformatics Institute (EBI) and in the international scientific community to develop new resources with value-added information. The SIFTS initiative is an example of such a collaboration—it provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases. SIFTS is widely used by major bioinformatics resources.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

ChEMBL: a large-scale bioactivity database for drug discovery (2011, background): “PDBBind (9), Binding MOAD (10) and AfﬁnDB (11) contain binding afﬁnity information for protein–ligand complexes found in the Protein Data Bank (PDB, 12).”
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource (2012, methodology): “For example, PDBeXplore allows browsing and analysis of the PDB archive on the basis of known biological and chemical classiﬁcation systems such as GO, Pfam, EC and taxonomy (6,24,25).”
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands (2015, background): “The number of GtoPdb ligands with a match to PDB structures is 17% (Figure 3, Row 11).”
FireDB: a compendium of biological and pharmacologically relevant ligands (2013, background): “FireDB clusters are cross-linked with UniProt accession codes (16) EC enzyme numbers (17) via MSD (18) and GO terms from GOA-PDB (19).”
UniProt Knowledgebase: a hub of integrated protein data (2011, background): “Building on the close collaboration which already exists between UniProtKB and the wwPDB, data related to interactions of proteins and small molecules will be imported from the PDBeMotif database (41).”
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (2017, methodology): “B.: MSD was rebranded in 2008 as the Protein Data Bank in Europe or PDBe [14, 19].)”
Global Guarantees for Enforcing Deep Generative Priors by Empirical Risk (2017, background): “In contrast, deep generative modeling simply requires obtaining a dataset of previously reconstructed molecular structures, which are easily available in extensive databases amassed over the years of practice of crystallography [76].”
The RCSB Protein Data Bank: new resources for research and education (2012, unknown): “org) (4), PDB Japan (PDBj, http://pdbj.”
Genenames.org: the HGNC resources in 2015 (2014, background): “‘Protein resources’ include a new link to PDBe (27) in addition to the links to UniProt and Interpro (28).”
Implementing an X-ray validation pipeline for the Protein Data Bank (2012, methodology): “A first glimpse of what could be performed with respect to analysis and validation of NMR entries is available as a PDBe service called Vivaldi (http:// pdbe.org/vivaldi; Velankar et al., 2012).”
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB (2015, background): “PDBeXplore (19), UniPDB (19), PDBePISA (20), PDBeMotif (21) and PDBeFold (22).”
Phospho.ELM: a database of phosphorylation sites—update 2011 (2010, background): “The PDB entry that was used to calculate the score, is listed in the second last column of the HTML output and is linked to the PDBe resource at the EBI where different viewers are available for closer inspection of the site.”