Additional file 1: of Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus

Table S1. The IAV-human network mined from the Intact, Virus Mint and virus Mentha; Table S2. The 110 RegExp asociated to human motif-domains interactions mined from 3-DID; Table S3. The amino acids motifs matched with the RegExp associated to human MDIs; Table S4. The amino acids motifs that matched an epitope in the immune epitope database; Table S5. The GO annotation and function of the 46 most frequently Motifs. (XLSX 979 kb

Comparison of methods of predicting HIV-human protein-protein interactions.

<p>Comparison of methods of predicting HIV-human protein-protein interactions.</p

Phenologs of human proteins non-targeted by virus.

<p>Phenologs of human proteins non-targeted by virus.</p

Predictions of interacting motifs on the amino acid sequence of VirC, NS5, NS3 and E proteins of the dengue virus serotype 2.

*<p>Numbering scheme for positions is according to the structures of VirC, NS3 and E proteins deposited in the PDB, PDB ID: 1R6R, 2VBC and 3UAJ, respectively. The numbering scheme used for the NS5 protein was according to the reported by Kumar et al., <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071526#pone.0071526-Kumar1" target="_blank">[55]</a>. E: exposed residue, and B: buried residue.</p

A Viral-Human Interactome Based on Structural Motif-Domain Interactions Captures the Human Infectome

<div><p>Protein interactions between a pathogen and its host are fundamental in the establishment of the pathogen and underline the infection mechanism. In the present work, we developed a single predictive model for building a host-viral interactome based on the identification of structural descriptors from motif-domain interactions of protein complexes deposited in the Protein Data Bank (PDB). The structural descriptors were used for searching, in a database of protein sequences of human and five clinically important viruses; therefore, viral and human proteins sharing a descriptor were predicted as interacting proteins. The analysis of the host-viral interactome allowed to identify a set of new interactions that further explain molecular mechanism associated with viral infections and showed that it was able to capture human proteins already associated to viral infections (human infectome) and non-infectious diseases (human diseasome). The analysis of human proteins targeted by viral proteins in the context of a human interactome showed that their neighbors are enriched in proteins reported with differential expression under infection and disease conditions. It is expected that the findings of this work will contribute to the development of systems biology for infectious diseases, and help guide the rational identification and prioritization of novel drug targets.</p></div

Examples of over-represent pathways targeted by viral proteins.

<p>Examples of over-represent pathways targeted by viral proteins.</p

Phenologs of human proteins targeted by virus.

<p>Phenologs of human proteins targeted by virus.</p

Analysis of the topological properties of the human proteins targeted and non-targeted by virus, respectively, in the context of a human interactome.

<p>The average degree, betweenness and shortest path length properties of human proteins targeted by virus (blue bars) are compared to that of human proteins non-targeted by virus (red bars).</p

Protocol for the prediction of the viral-human interactome based on structural motif-domain interactions.

<p>Protocol for the prediction of the viral-human interactome based on structural motif-domain interactions.</p

Comparison of Arabidopsis and human phenologs associated to pathogen responses and human phenotype, respectively.

<p>Comparison of Arabidopsis and human phenologs associated to pathogen responses and human phenotype, respectively.</p