ProCarbDB: A Database of Carbohydrate-binding Proteins
Nucleic Acids Research
Oxford University Press
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Copoiu, L., Torres, P. H., Asher, D. B., Blundell, T., & Malhotra, S. (2019). ProCarbDB: A Database of Carbohydrate-binding Proteins. Nucleic Acids Research https://doi.org/10.1093/nar/gkz860
Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their three-dimensional structures are reported, has led to difficulties in characterising the protein-carbohydrate interfaces. In order to better understand protein-carbohydrate interactions, we have developed an open-access database, ProCarbDB, which, unlike the Protein Data Bank (PDB), clearly distinguishes between the complete carbohydrate ligands and their monomeric units. ProCarbDB is a comprehensive database containing over 5200 three-dimensional X-ray crystal structures of protein-carbohydrate complexes. In ProCarbDB the complete carbohydrate ligands are annotated and all their interactions are displayed. Users can also select any protein residue in the proximity of the ligand to inspect its interactions with the carbohydrate ligand and with other neighbouring protein residues. Where available, additional curated information on the binding affinity of the complex and the effects of mutations on the binding have also been provided in the database. We believe that ProCarbDB will be an invaluable resource for understanding protein-carbohydrate interfaces. The ProCarbDB web server is freely available at http://www.procarbdb.science/procarb.
L.C. was supported by a Collaborative Award in Science and Engineering from Ipsen Bioinnovation Ltd. to support his Research towards a PhD. D.B.A was supported by the Jack Brockhoff Foundation [JBF 4186, 2016] and the National Health and Medical Research Council of Australia [APP1072476]. P.H.M.T. was supported by The Cystic Fibrosis Trust (SRC 010 - RG92232). D.B.A and T.L.B were supported by a Newton Fund RCUK-CONFAP Grant awarded by The Medical Research Council (MRC) [MR/M026302/1].
External DOI: https://doi.org/10.1093/nar/gkz860
This record's URL: https://www.repository.cam.ac.uk/handle/1810/297865
Attribution 4.0 International
Licence URL: http://creativecommons.org/licenses/by/4.0/
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