About one third of the known proteins are predicted to be disordered, both as fully disordered proteins or as a harlequin of structured and disordered regions. These disordered regions (IDR) participate in interactions with multiple ligands, that can come about through disorder-order transitions using Molecular Recognition Features (MoRFs), or keeping an important degree of disorder in the complex (fuzzy complexes). Using molecular dynamics simulations, we model the structural ensemble of two IDRs, one that may present a MoRF (the transcription factor Escargot from Drosophila melanogaster, with a ~300 amino acid-long disordered N-terminal domain, within which we identified a 45 amino acid region with increased proneness to order) and one that most likely engages in fuzzy complexes (the adenovirus protein E1B55kDa, with a disordered C-terminal peptide, highly charged and susceptible to phosphorylation). We characterize the residual structure in these ensembles and the effect that both mutations and post-translational modifications have on these, in an attempt to localize putative binding sites that could be validated experimentally.