Project ranks billions of drug interactions

by Sabrina I. Pacifici on December 1, 2013

Drugable.com predicts mechanisms through computation: “For decades, drug development was mostly a game of trial and error, with brute-force candidate screens throwing up millions more duds than winners. Researchers are now using computers to get a head start. By analysing the chemical structure of a drug, they can see if it is likely to bind to, or ‘dock’ with, a biological target such as a protein. Such algorithms are particularly useful for finding potentially toxic side effects that may come from unintended dockings to structurally similar, but untargeted, proteins. Last week, researchers presented a computational effort that assesses billions of potential dockings on the basis of drug and protein information held in public databases. “It’s the largest computational docking ever done by mankind,” says Timothy Cardozo, a pharmacologist at New York University’s Langone Medical Center, who presented the project on 19 November at the US National Institutes of Health’s High Risk–High Reward Symposium in Bethesda, Maryland. The result, a website called Drugable that is backed by the US National Library of Medicine (NLM), is still in testing, but it will eventually be available for free, allowing researchers to predict how and where a compound might work in the body, purely on the basis of chemical structure (see ‘Mining for drugs’)…Predicting how untested compounds will interact with proteins in the body, as Drugable attempts to do, is more challenging. In setting up the website, Cardozo’s group selected about 600,000 molecules from PubChem and the European Bioinformatics Institute’s ChEMBL, which together catalogue millions of publicly available compounds. The group evaluated how strongly these molecules would bind to 7,000 structural ‘pockets’ on human proteins also described in the databases. Computing giant Google awarded the researchers the equivalent of more than 100 million hours of processor time on its supercomputers for the mammoth effort.”

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