Waman, VP;
Orengo, C;
Kleywegt, GJ;
Lesk, AM;
(2021)
Three-dimensional Structure Databases of Biological Macromolecules.
Data Mining Techniques for the Life Sciences. Methods in Molecular Biology
, 2449
pp. 43-91.
10.1007/978-1-0716-2095-3_3.
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Abstract
Databases of three-dimensional structures of proteins (and their associated molecules) provide: (a)Curated repositories of coordinates of experimentally determined structures, including extensive metadata; for instance information about provenance, details about data collection and interpretation, and validation of results.(b)Information-retrieval tools to allow searching to identify entries of interest and provide access to them.(c)Links among databases, especially to databases of amino-acid and genetic sequences, and of protein function; and links to software for analysis of amino-acid sequence and protein structure, and for structure prediction.(d)Collections of predicted three-dimensional structures of proteins. These will become more and more important after the breakthrough in structure prediction achieved by AlphaFold2. The single global archive of experimentally determined biomacromolecular structures is the Protein Data Bank (PDB). It is managed by wwPDB, a consortium of five partner institutions: the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB), the Protein Data Bank Japan (PDBj), the BioMagResBank (BMRB), and the Electron Microscopy Data Bank (EMDB). In addition to jointly managing the PDB repository, the individual wwPDB partners offer many tools for analysis of protein and nucleic acid structures and their complexes, including providing computer-graphic representations. Their collective and individual websites serve as hubs of the community of structural biologists, offering newsletters, reports from Task Forces, training courses, and “helpdesks,” as well as links to external software. Many specialized projects are based on the information contained in the PDB. Especially important are SCOP, CATH, and ECOD, which present classifications of protein domains.
| Type: | Article |
|---|---|
| Title: | Three-dimensional Structure Databases of Biological Macromolecules |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1007/978-1-0716-2095-3_3 |
| Publisher version: | https://doi.org/10.1007/978-1-0716-2095-3_3 |
| Language: | English |
| Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions. |
| Keywords: | Data archiving, Domain analysis, Fold classification, Protein Data Bank, Protein structure, Structural biology, Computational Biology, Databases, Protein, Protein Conformation, Proteins, Software |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10171965 |
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