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PDBe: towards reusable data delivery infrastructure at protein data bank in Europe
S. Mir, Y. Alhroub, S. Anyango, DR. Armstrong, JM. Berrisford, AR. Clark, MJ. Conroy, JM. Dana, M. Deshpande, D. Gupta, A. Gutmanas, P. Haslam, L. Mak, A. Mukhopadhyay, N. Nadzirin, T. Paysan-Lafosse, D. Sehnal, S. Sen, OS. Smart, M. Varadi, GJ....
Language English Country England, Great Britain
Document type Journal Article, Research Support, Non-U.S. Gov't
Grant support
104948
Wellcome Trust - United Kingdom
BB/M011674/1
Biotechnology and Biological Sciences Research Council - United Kingdom
BB/N019172/1
Biotechnology and Biological Sciences Research Council - United Kingdom
BB/M020347/1
Biotechnology and Biological Sciences Research Council - United Kingdom
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PubMed
29126160
DOI
10.1093/nar/gkx1070
Knihovny.cz E-resources
- MeSH
- Molecular Sequence Annotation MeSH
- Databases as Topic MeSH
- Databases, Protein * MeSH
- Internet MeSH
- Protein Conformation, alpha-Helical MeSH
- Protein Conformation, beta-Strand MeSH
- Humans MeSH
- Models, Molecular MeSH
- Computer Graphics MeSH
- Proteins chemistry genetics metabolism MeSH
- Amino Acid Sequence MeSH
- Sequence Analysis, Protein methods MeSH
- Information Dissemination MeSH
- User-Computer Interface * MeSH
- Computational Biology methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Europe MeSH
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
References provided by Crossref.org
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