To which proteins does a compound bind? Is it selective or promiscuous? These are questions which can be answered by inverse virtual screening, which identifies potential targets for a molecule of interest. Experimental screening of a molecule on thousands of targets is costly and elaborate. Contrarily, structure-based computational methods are only limited by the availability of 3D structures,...

MOTIVATION Pairing between the target sequence and the 6-8 nt long seed sequence of the miRNA presents the most important feature for miRNA target site prediction. Novel high-throughput technologies such as Argonaute HITS-CLIP afford meanwhile a detailed study of miRNA:mRNA duplices. These interaction maps enable a first discrimination between functional and non-functional target sites in a bul...

In this chapter, we review evidence that at least three different types of microRNA (miRNA)-messenger RNA (mRNA) target interactions exist in mammals: short seeds, long seeds, and "perfect" hits (allowing G:U matches). Because new types of miRNAs are still being discovered, this list may not yet be complete.