PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

By S. Velankar, G. V. Ginkel, Younes Alhroub, G. Battle, J. Berrisford, M. J. Conroy, J. M. Dana, Swanand P. Gore, A. Gutmanas, Pauline Haslam and 23 more. 2015

126 citations recorded by the source corpus.

The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the ‘best structures’ for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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Citations in the corpus

SWISS-MODEL: homology modelling of protein structures and complexes (2018, neutral): “We include links to the RCSB (33), PDBsum (40), PDBe (41), CATH (42) and SwissDock (43).”
InterPro in 2017—beyond protein family and domain annotations (2016, background): “Its data feed into a host of annotation pipelines, including ENSEMBL (26), ENSEMBL Genomes (27), PDBe (28), BLAST2GO (29), PhytoPath (30), the digenic diseases database - DIDA (31), and the Endeavour candidate gene prioritisation server (32).”
MobiDB‐lite: fast and highly specific consensus prediction of intrinsic disorder in proteins (2017, methodology): “More recently, the MobiDB database (Di Domenico et al., 2012; Potenza et al., 2015) has been established as a centralized resource collecting annotations for all UniProt (UniProt Consortium, 2014) entries based on different definitions of ID, including manually curated information from DisProt (Piov”
PDBe: improved findability of macromolecular structure data in the PDB (2019, background): “In 2015, PDBe introduced a new query system (31), providing innovative and intuitive search options for accessing PDB data.”
PDBsum: Structural summaries of PDB entries (2017, background): “uk/ pdbe.(15) Both offer a comprehensive and detailed coverage of all PDB entries together with some powerful resources for structural analysis.”
The RCSB protein data bank: integrative view of protein, gene and 3D structural information (2016, background): “org) (5), plus a global nuclear magnetic resonance (NMR) specialist data repository BioMagResBank, composed of deposition sites in the US (BMRB; http://www.”
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation (2016, background): “Transitive links are also imported including links from UniProt to PDBe (36).”
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures (2016, methodology): “Regions, units and insertions are provided for all entries and correctly mapped both to UniProt and PDB reference (SEQRES field in the PDB file) sequences thanks to the SIFTS service.”
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (2017, methodology): “Following a transition period that witnessed formalization of Protein Data Bank Japan (PDBj) [12] and the Macromolecular Structure Database (MSD) [13, 14], RCSB PDB, PDBj, and MSD came together in 2003 to establish the Worldwide Protein Data Bank (wwPDB; wwpdb.org) [ 15].”