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Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes.

Pires DE, Blundell TL, Ascher DB - Nucleic Acids Res. (2014)

Bottom Line: Drug resistance is a major challenge for the treatment of many diseases and a significant concern throughout the drug development process.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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK dpires@dcc.ufmg.br.

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Architecture of data integration and curation of Platinum.
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Figure 1: Architecture of data integration and curation of Platinum.

Mentions: Ligand properties such as molecular weight, logP, number of hydrogen acceptors and donors were calculated using RDKit and complementary ligand information such as Canonical Smiles and ligand type were obtained from the PDBeChem (22). All entries were manually double-checked, with additional filters used to confirm the correctness of all structural and affinity information. Figure 1 shows the workflow for data collection and curation used to build Platinum.


Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes.

Pires DE, Blundell TL, Ascher DB - Nucleic Acids Res. (2014)

Architecture of data integration and curation of Platinum.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384026&req=5

Figure 1: Architecture of data integration and curation of Platinum.
Mentions: Ligand properties such as molecular weight, logP, number of hydrogen acceptors and donors were calculated using RDKit and complementary ligand information such as Canonical Smiles and ligand type were obtained from the PDBeChem (22). All entries were manually double-checked, with additional filters used to confirm the correctness of all structural and affinity information. Figure 1 shows the workflow for data collection and curation used to build Platinum.

Bottom Line: Drug resistance is a major challenge for the treatment of many diseases and a significant concern throughout the drug development process.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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK dpires@dcc.ufmg.br.

Show MeSH
Related in: MedlinePlus