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

Velankar, Sameer; Ginkel, Glen van; Alhroub, Younes; Battle, Gary M.; Berrisford, John M.; Conroy, Matthew J.; Dana, Jose M.; Gore, Swanand; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter; Lagerstedt, Ingvar; Mir, Saqib; Montecelo, Manuel A Fernandez; Mukhopadhyay, Abhik; Oldfield, Thomas J.; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, R.; Wainwright, Michael; Deshpande, Mandar; Iudin, A.; Sahni, Gaurav; Salavert-Torres, José; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David; Clark, Alice R.; Smart, Oliver S.; Korir, Paul K; Kleywegt, Gerard J.

doi:10.1093/nar/gkv1047

Cited by 143 publications

(103 citation statements)

References 52 publications

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“…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). The InterProScan Web services are extensively used, processing in excess of 40 million sequence searches per month.…”

Section: Introductionmentioning

confidence: 99%

InterPro in 2017—beyond protein family and domain annotations

et al. 2016

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InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences.

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Section: Introductionmentioning

confidence: 99%

InterPro in 2017—beyond protein family and domain annotations

et al. 2016

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“…Long non-coding RNA (lncRNA) coverage was extended by the addition of NONCODE (15) and LNCipedia (16) datasets. The inclusion of PDB (17) as an Expert Database helps to map between the worlds of ncRNA sequence and structure. Small nucleolar RNAs (snoRNAs) play an important role in guiding the modification of other ncRNA and mRNAs (18), and snoPY (19) provides to RNAcentral a dataset of snoRNAs found in human, fly, worm, yeast, and thale cress.…”

Section: Data Overviewmentioning

confidence: 99%

RNAcentral: a comprehensive database of non-coding RNA sequences

Petrov¹,

Kay²,

Kalvari³

et al. 2016

Nucleic Acids Research

203

109

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RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.

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“…The RCSB PDB has extensive search and reporting capabilities as well as an education portal called PDB-101 [26,29]. PDBe has multiple search and browse facilities as well as analysis and bioinformatics tools [30,31]. PDBj provides a variety of services and viewers and supports browsing in multiple Asian languages [23,32].…”

Section: Value-added Resourcesmentioning

confidence: 99%

The archiving and dissemination of biological structure data

Berman

Burley

Kleywegt³

et al. 2016

Current Opinion in Structural Biology

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The global Protein Data Bank (PDB) was the first open-access digital archive in biology. The history and evolution of the PDB are described, together with the ways in which molecular structural biology data and information are collected, curated, validated, archived, and disseminated by the members of the Worldwide Protein Data Bank organization (wwPDB; http://wwpdb.org). Particular emphasis is placed on the role of community in establishing the standards and policies by which the PDB archive is managed day-to-day.

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

Cited by 143 publications

References 52 publications

InterPro in 2017—beyond protein family and domain annotations

InterPro in 2017—beyond protein family and domain annotations

RNAcentral: a comprehensive database of non-coding RNA sequences

The archiving and dissemination of biological structure data

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