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. 2020 Jan 8;48(D1):D335-D343.
doi: 10.1093/nar/gkz990.

PDBe: improved findability of macromolecular structure data in the PDB

David R Armstrong  1 , John M Berrisford  1 , Matthew J Conroy  1 , Aleksandras Gutmanas  1 , Stephen Anyango  1 , Preeti Choudhary  1 , Alice R Clark  1 , Jose M Dana  1 , Mandar Deshpande  1 , Roisin Dunlop  1 , Paul Gane  1 , Romana Gáborová  2 , Deepti Gupta  1 , Pauline Haslam  1 , Jaroslav Koča  2 , Lora Mak  1 , Saqib Mir  1 , Abhik Mukhopadhyay  1 , Nurul Nadzirin  1 , Sreenath Nair  1 , Typhaine Paysan-Lafosse  1   3 , Lukas Pravda  1 , David Sehnal  2 , Osman Salih  4 , Oliver Smart  1 , James Tolchard  1 , Mihaly Varadi  1 , Radka Svobodova-Vařeková  2 , Hossam Zaki  1 , Gerard J Kleywegt  1   4 , Sameer Velankar  1
Affiliations

PDBe: improved findability of macromolecular structure data in the PDB

David R Armstrong et al. Nucleic Acids Res. .

Abstract

The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.

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Figures

Figure 1.
Figure 1.
(A) Image of cholesterol (PDB three-letter code: CLR) generated from the PDB Chemical Component Dictionary, using the pdbeccdutils process. (B) Chemical scaffold (in green) of cholesterol, identified and highlighted using the pdbeccdutils process.
Figure 2.
Figure 2.
New features added to the PDBe search. (A) The advanced search form supports 122 fields in queries. (B) Sequence searching using HMMER. (C) Autocomplete option to find relevant search terms for each search field.
Figure 3.
Figure 3.
New features in presenting search results, including: number of facets (left) increased to 39 to improve filtering of results, access to 3D visualization and file downloads directly from the search results (green text); alignment and statistics provided for sequence searches, links to PDBe-KB aggregated views.
Figure 4.
Figure 4.
Improved visualization of nucleic acids and carbohydrates in LiteMol. (A) PDB entry 5ezi (48), the structure of a malaria antigen in complex with an antibody, focused on the branched glycan in the structure. The glycan is shown using the 3D-SNFG representation. (B) PDB entry 5x2g (49), structure of a CRISPR-Cas9 complex of protein with nucleic acids, using the new visualization for RNA and DNA.
See this image and copyright information in PMC

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