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Open Access Highly Accessed Methodology

Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria

Phelelani T Mpangase, Michal J Szolkiewicz, Misha le Grange, Jeanré H Smit, Pieter B Burger and Fourie Joubert*

Author Affiliations

Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria 0001, South Africa

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Malaria Journal 2013, 12:116  doi:10.1186/1475-2875-12-116

Published: 28 March 2013

Abstract

Background

Drug resistance to anti-malarial compounds remains a serious problem, with resistance to newer pharmaceuticals developing at an alarming rate. The development of new anti-malarials remains a priority, and the rational selection of putative targets is a key element of this process. Discovery-2 is an update of the original Discovery in silico resource for the rational selection of putative drug target proteins, enabling researchers to obtain information for a protein which may be useful for the selection of putative drug targets, and to perform advanced filtering of proteins encoded by the malaria genome based on a series of molecular properties.

Methods

An updated in silico resource has been developed where researchers are able to mine information on malaria proteins and predicted ligands, as well as perform comparisons to the human and mosquito host characteristics. Protein properties used include: domains, motifs, EC numbers, GO terms, orthologs, protein-protein interactions, protein-ligand interactions. Newly added features include drugability measures from ChEMBL, automated literature relations and links to clinical trial information. Searching by chemical structure is also available.

Results

The updated functionality of the Discovery-2 resource is presented, together with a detailed case study of the Plasmodium falciparum S-adenosyl-L-homocysteine hydrolase (PfSAHH) protein. A short example of a chemical search with pyrimethamine is also illustrated.

Conclusion

The updated Discovery-2 resource allows researchers to obtain detailed properties of proteins from the malaria genome, which may be of interest in the target selection process, and to perform advanced filtering and selection of proteins based on a relevant range of molecular characteristics.