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iPHACE from the UPF, a tool to see the interactions of drugs with proteins

On 15 February, the international journal Bioinformatics, specializing in the field of mathematics and computational biology, published an article about a web application developed by the Laboratory of chemogenomics, directed by Jordi Mestres, within the Research Group on Biomedical Informatics ( GRIB) at the UPF-IMIM. Entitled "iPHACE: integrative navigation in pharmacological space" the article describes the features of this new tool with which one can graphically explore a space generated by the interactions of drugs with proteins for which they have an affinity.

2 March 2010

Historically, the few resources devoted to the study of pharmacological profiles on large sets of proteins and the high costs of these experiments have led to the idea that the drugs acted selectively on one or a few target proteins. Currently, the cutting down of the costs and the emergence of various initiatives to compile public information hitherto scattered in articles in this field have resulted in the creation of large interaction data repositories that grow day by day.

This data is routinely consulted on independent websites but to analyze this large volume of information and gain a global view it is necessary to develop new integrated tools. With this intention iPHACE developed, which in its first version contains information of about 750 drugs towards 180 target proteins.

The first step is to capture the relevant information contained in different storage systems or repositories and provide a common format. Then, the different elements are sorted according to appropriate classification schemes and which are then presented to the user to extract the associated information associated. Once done, the data is loaded into the database of the tool and from that point; one can freely consult it across the web.

iPHACE allows, for example, viewing the list of proteins associated with drugs that have affinity for a specific target protein. At the same time, by applying a filter structure, one can study which are the target proteins of the drugs that contain a specific chemical structure. Going further, one of the most innovative features of this application is the ability to compare the pharmacological profiles of different drugs, which can highlight relationships than if the individually affinities are considered would pass unnoticed.



Reference:
Ricard Garcia-Serna, Oleg Ursu, Tudor I. Oprea and Jordi Mestres (2010), " iPHACE: integrative navigation in pharmacological space", Bioinformatics, doi: 10.1093/bioinformatics/btq061.

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