Platinum


NAR Molecular Biology Database Collection entry number 1780
Ascher, David; Pires, Douglas; Blundell, Tom
Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK

Database Description

The ability to understand and predict the effects of mutations on protein–ligand affinities and their roles in the emergence of resistance would significantly aid treatment and drug design strategies. In order to study and understand the impacts of missense mutations on the interaction of ligands with the proteome, we have developed Platinum (http://structure.bioc.cam.ac.uk/platinum). This manually curated, literature-derived database, comprising over 1000 mutations, associates for the first time experimental information on changes in affinity with three-dimensional structures of protein–ligand complexes. To minimize differences arising from experimental techniques and to directly compare binding affinities, Platinum considers only changes measured by the same group and with the same amino-acid sequence used for structure determination, providing a direct link between protein structure, how a ligand binds and how mutations alter the affinity of the ligand of the protein. In order to account for additional consequences of the mutations, the predicted effects of single point mutations on protein stability (1) and protein-protein affinity (2) in the three-dimensional structure were calculated when a wild-type PDB structure was available. We believe Platinum will be an invaluable resource for understanding the effects of mutations that give rise to drug resistance, a major problem emerging in pandemics including those caused by the influenza virus, in infectious diseases such as tuberculosis, in cancer and in many other life-threatening illnesses.

Acknowledgements

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil [to D.E.V.P.]; NHMRC CJ Martin Fellowship [APP1072476 to D.B.A.]; University of Cambridge and The Wellcome Trust for facilities and support [to T.L.B.].

References

1. Pires D.E.V., Ascher D.B., Blundell T.L. DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. 2014;42:W314-W319.
2. Pires D.E.V., Ascher D.B., Blundell T.L. mCSM: predicting the effects of mutations in proteins using graph-based signatures. 2014;30:335-342.

Subcategory: Protein structure

Go to the abstract in the NAR 2015 Database Issue.
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