We have used multivariate statistics and z-scales to represent peptide sequences in a PLS-QSAR model of previously studied binding affinities [Kofler,M., Motzny,K. and Freund,C. (2005b) Mol. Cell. Proteomics, 4, 1797-1811.] of two GYF domains to an array of immobilized synthetic peptides. As a result, we established structural determinants of the binding specificities of the two proteins. Our model was used to define new sets of yeast proteins potentially interacting with Syh1 (YPL105C) and Smy2 (YBR172C). These sets were subsequently examined for co-occurrence of Gene Ontology terms, leading to suggest a group of likely interacting proteins with a common function in mRNA catabolism. Finally, subcellular localization of a GFP-fused Syh1 and Smy2 reinforced the possibility that these proteins reside in cytoplasmic sites of mRNA degradation, thereby providing experimental confirmation to the predictions from the model.