When drug discovery meets web search: Learning to Rank for ligand-based virtual screening

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>The rapid increase in the emergence of novel chemical substances presents a substantial demands for more sophisticated computational methodologies for drug discovery. In this study, the idea of <jats:italic>Learning to Rank</jats:italic> in web search was presented in drug virtual screening, which has the following unique capabilities of 1). Applicable of identifying compounds on novel targets when there is not enough training data available for these targets, and 2). Integration of heterogeneous data when compound affinities are measured in different platforms.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>A standard pipeline was designed to carry out <jats:italic>Learning to Rank</jats:italic> in virtual screening. Six <jats:italic>Learning to Rank</jats:italic> algorithms were investigated based on two public datasets collected from Binding Database and the newly-published Community Structure-Activity Resource benchmark dataset. The results have demonstrated that <jats:italic>Learning to rank</jats:italic> is an efficient computational strategy for drug virtual screening, particularly due to its novel use in cross-target virtual screening and heterogeneous data integration.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>To the best of our knowledge, we have introduced here the first application of <jats:italic>Learning to Rank</jats:italic> in virtual screening. The experiment workflow and algorithm assessment designed in this study will provide a standard protocol for other similar studies. All the datasets as well as the implementations of <jats:italic>Learning to Rank</jats:italic> algorithms are available at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.tongji.edu.cn/~qiliu/lor_vs.html" ext-link-type="uri">http://www.tongji.edu.cn/~qiliu/lor_vs.html</jats:ext-link>.</jats:p> </jats:sec>