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Background  Short linear motifs in host organisms proteins can be mimicked by viruses to create protein-protein interactions that disable or control metabolic pathways. Given that viral linear motif instances of host motif regular expressions can be found by chance, it is necessary to develop filtering methods of functional linear motifs. We conduct a systematic comparison of linear motifs filtering methods to develop a computational approach for predicting motif-mediated protein-protein interactions between human and the human immunodeficiency virus 1 (HIV-1).    Results  We implemented three filtering methods to obtain linear motif sets: 1) conserved in viral proteins ( C ), 2) located in disordered regions ( D ) and 3) rare or scarce in a set of randomized viral sequences ( R ). The sets  C,D,R  are united and intersected. The resulting sets are compared by the number of protein-protein interactions correctly inferred with them – with experimental validation. The comparison is done with HIV-1 sequences and interactions from the National Institute of Allergy and Infectious Diseases (NIAID).  The number of correctly inferred interactions allows to rank the interactions by the sets used to deduce them:  D ∪ R  and  C . The ordering of the sets is descending on the probability of capturing functional interactions.  With respect to HIV-1, the sets  C ∪ R ,  D ∪ R ,  C ∪ D ∪ R  infer all known interactions between HIV1 and human proteins mediated by linear motifs. We found that the majority of conserved linear motifs in the virus are located in disordered regions.    Conclusion  We have developed a method for predicting protein-protein interactions mediated by linear motifs between HIV-1 and human proteins. The method only use protein sequences as inputs. We can extend the software developed to any other eukaryotic virus and host in order to find and rank candidate interactions. In future works we will use it to explore possible viral attack mechanisms based on linear motif mimicry.    Electronic supplementary material  The online version of this article (doi:10.1186/s12859-017-1570-7) contains supplementary material, which is available to authorized users.

Prediction of virus-host protein-protein interactions mediated by short linear motifs