TABLE 5.

A non-exhaustive catalog of resources, tools and databases to compile protein–protein interaction based workflows for inferring microbe (microbiome)-host interactions.

Step in workflow	Resource/Tool/Database
Source of proteomes (sequence information)	UniProt (The UniProt Consortium, 2018), HumanPSD (Hodges et al., 2002), YPD (Payne and Garrels, 1997), PombePD (Costanzo et al., 2001), WormPD (Costanzo et al., 2001), and SWISS-PROT (Bairoch and Apweiler, 1996)
Source of proteomic datasets (expression information)	ProteomicsDB (Schmidt et al., 2018), Human Protein Atlas (HPA) (Thul and Lindskog, 2018), PRIDE (Perez-Riverol et al., 2019), PeptideAtlas (Desiere et al., 2006), MassIVE.quant (Choi et al., 2020), jPOSTrepo (Okuda et al., 2017), iProX (Ma et al., 2019), and Panorama Public (Sharma et al., 2018)
Proteomic annotations (structural features)	InterPro (Mitchell et al., 2019), Pfam (El-Gebali et al., 2019), ELM (Gouw et al., 2018), and PDB (Burley et al., 2017)
Protein sub-cellular localization (databases and prediction tools)	ComPPI (Veres et al., 2015), HPA (Thul and Lindskog, 2018), LocDB (Rastogi and Rost, 2011), LocSigDB (Negi et al., 2015), COMPARTMENTS (Binder et al., 2014), eSLDB (Pierleoni et al., 2007), SCLpred-EMS (Kaleel et al., 2020), DeepLoc (Almagro Armenteros et al., 2017), PSORTdb (Peabody et al., 2016), SecretomeP (Bendtsen et al., 2004), and Signal P (Armenteros et al., 2019)
Base information for prediction of PPIs	Domain-domain predictions – DOMINE (Raghavachari et al., 2008) and Domain-motif predictions – ELM (Gouw et al., 2018)
Quality control of inferred PPIs (using disordered region prediction)	IUPred (Mészáros et al., 2018), PrDOS (Ishida and Kinoshita, 2007), D2P2 (Oates et al., 2013), PONDR-FIT (Xue et al., 2010), DISOPRED (Ward et al., 2004), MFDp2 (Mizianty et al., 2013), and Meta-Disorder (Kozlowski and Bujnicki, 2012)
Network resources	OmniPath (Türei et al., 2016), IntAct (Orchard et al., 2014), Reactome (Fabregat et al., 2018), STRING (Szklarczyk et al., 2017), HTRI (Bovolenta et al., 2012), and DoRothEA (Garcia-Alonso et al., 2018)
Network diffusion approaches	NBS (Hofree et al., 2013), HotNet (Vandin et al., 2011), TieDie (Basha et al., 2013; Paull et al., 2013), RegMod (Qiu et al., 2010), and stSVM21 (Cun and Fröhlich, 2013)
Databases for host gene expression	GEO (Clough and Barrett, 2016) and ArrayExpress (Parkinson et al., 2007)