Hello, On Tue, Jun 12, 2012 at 12:32 PM, David Wild <djw...@indiana.edu> wrote: >> Hopefully, in the future, we will be able to simulate, for a given >> chemical structure: >> >> - which proteins (or other bio-molecules) it interacts with >> - how that interaction changes the function of the bio-molecule >> - how changed function of molecules change biological networks and >> systemic function >> >> However, what the article says sounds more limited: >> >> "... a database of 73 proteins ..." >> >> > As such, Open Linked Data might offer help! >> >> Eventually. > > > The first (drug-target prediction) is something we're working on at IU - > using a large, heterogenous semantic network of public compound, target, > gene, expression, pathway, disease data to make drug-target predictions (see > http://chem2bio2rdf.org/slap > , http://slapfordrugtargetprediction.wikispaces.com/ , paper in press at > PLoS Comp. Bio.). Results are promising so far but biggest question is how > you weight different kinds of paths, nodes and edges - there is no one > correct answer, but is dependent on the scientist and application using it. > Right now we're not claiming that it predicts compound-target binding but > rather an "association" which deserves further investigation. Also have to > address preconception by many that "large / integrated dataset" = low > quality, high errors. I argue that if you read 5 papers a day you are > overall better informed than if you read just one of them, even if that one > paper is a very high quality newspaper.
Interesting tool! I'm not sure I'm using it correctly, though: I entered sulfuric acid and insulin, and it found no direct interaction, although I am pretty sure sulfuric acid directly reacts with insulin. Take care Oliver -- Oliver Ruebenacker Bioinformatics Consultant (http://www.knowomics.com/wiki/Oliver_Ruebenacker) Knowomics, The Bioinformatics Network (http://www.knowomics.com) SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)