EvoPPI 2: A Web and Local Platform for the Comparison of Protein–Protein Interaction Data from Multiple Sources from the Same and Distinct Species

On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3

“…As shown in Reboiro-Jato et al. [ 17 ], the H. sapiens Ataxin-1 PPI network reported in the main databases, although large (380 interactions), is still incomplete, since the predicted interactome of H. sapiens based on M. musculu s is much larger (1243 and 592 interactions when considering the DIOPT or Ensembl M. musculu s – H. sapiens orthologies, respectively) than the one reported in humans. Therefore, using the new EvoPPI3 datasets, we try to get a better estimate of the size and composition of the Ataxin-1 PPI network.…”

“…For a given pair of proteins, PPI can also be addressed using methods such as X-ray crystallography, NMR spectroscopy, fluorescence resonance energy transfer (FRET), and surface plasmon resonance (SPR) [ 2 ]. These interactions are compiled in primary databases such as BioGRID [ 3 , 4 ], CCSB [ 5 ], DroID [ 6 ], FlyBase [ 7 ], HIPPIE [ 8 ], HitPredict [ 9 ], HomoMINT [ 10 ], Instruct [ 11 ], Interactome3D [ 12 ], Mentha [ 13 ], MINT [ 14 ], and PINA v2 [ 15 ], all included in EvoPPI [ 16 , 17 ], a meta-database, for PPI. Although these are literature-curated databases, false positive interactions may still be reported, mainly due to the experimental limitations of the methods used to characterize PPI.…”