The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

By Peter W. Rose, Andreas Prlic, Chunxiao Bi, Wolfgang Bluhm, Cole H. Christie, Shuchismita Dutta, Rachel Kramer Green, David S. Goodsell, John D. Westbrook, Jesse Woo and 5 more. Nucleic Acids Res., 2014

509 citations recorded by the source corpus.

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5058717ad996ea0b56dceb79d61588690a166b28

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Citations in the corpus

A comprehensive review and comparison of different computational methods for protein remote homology detection (2018, unknown): “The number of proteins in these families varies significantly, for example in SCOPe 2.06, there are only 28 PDB entries in family a.1.1.1, while protein family a.1.1.2 has 1274 PDB entries, leading to an extremely class-imbalanced problem.”
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database (2016, background): “In addition to expanding the conceptual framework of the ARO to cover the breadth of AMR mechanisms, curators also associate ARO terms with the relevant publications, chemical structures (via curation of PubChem information), and protein structures (via curation of Protein Data Bank information (16)”
CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides (2015, methodology): “Links to UniPro-tKB, PDB, PubMed (12) and other databases dedicated to AMPs are also made available for the benefit of the users.”
CATH: an expanded resource to predict protein function through structure and sequence (2016, background): “CATH identifies protein domain structures within protein threedimensional (3D) structures from the Protein Data Bank (PDB) (2) and assigns domains sharing evolutionary similarities to the same superfamily within the CATH hierarchical structure classification.”
Origins of coevolution between residues distant in protein 3D structures (2017, background): “Around three-fourths of multimeric biological units in PDB represent homo-oligomeric assemblies (26), and coevolution occurs at homo-oligomeric interfaces (27), leading to contact predictions by GREMLIN across interfaces.”
KLIFS: a structural kinase-ligand interaction database (2015, unknown): “All sequences from human (490) and mouse (525) eukaryotic protein kinases, the two most prevalent species in published kinase structures, are used as input for a BLAST query (10) against all structures released by the PDB (Figure 1).”
CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides (2015, methodology): “If the peptide was not available in PDB, we predicted the structure of those peptides using structure prediction techniques.”
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics (2020, background): “org) (31) is also queried to identify experimentally determined 3D structures of AMPs.”
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules (2016, methodology): “In the previous version, when only the sequence (rather than the structure) of the query protein was provided as input (i.e. ‘ConSeq mode’), ConSurf searched the PDB (52,53) us-ing BLAST (54) to suggest probable homologues of known structure.”
Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis (2017, background): “In addition, we required that at least one high-resolution protein structure be deposited in the Protein Data Bank (PDB) (29) to distinguish coevolving intraprotein from interprotein contacts as further discussed below.”
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology (2015, methodology): “The bidirectional links between BindingDB and the RCSB (10) Protein Data Bank (PDB) (11,12) are probably the most heavily used: the home pages for many crystal structures in the PDB are hyperlinked to the corresponding protein–small molecule affinity data in BindingDB, and, conversely, many…”
The Transporter Classification Database (TCDB): recent advances (2015, background): “RCSP PDB (26) Provides high-resolution crystal or NMR structures for transport proteins when available Interpro (27) Provides functional analysis of transporters by classifying them according to domains and other important sites or motifs”
The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology (2015, background): “The RCSB PDB [7] offers both expert (http://www.”
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins – extended Database (2016, methodology): “We use a combination of manual curation and a rigorously validated software pipeline [5] to add new structures from the Protein Data Bank (PDB) [6,7], and we have also developed software to identify errors in SCOP, which are then corrected in new releases of SCOPe.”