Human Tissue-specific Protein-Protein Interactions (TS-PPI)
Human TS-PPI is compiled by integrating non-redundant human protein-protein interaction (PPI) data with gene expression data. The union of interactions stored in publicly available, literature curated databases: BioGrid (Stark et al. 2011), DIP (Salwinski et al. 2004) , HPRD (Prasad et al. 2009), IntAct (Aranda et al. 2010) and MINT (Ceol et al. 2010) was considered as human PPI. The microarray gene expression data is available for 84 tissues as ‘Human U133A/GNF1H Gene Atlas’ at BioGPS(http://biogps.org) (Wu et al. 2009). Only 70 normal tissues were considered for TS-PPI and the disease and the fetal tissues were ignored. This dataset is available for download as tab delimited text file (TS-PPI.txt).
Human-Virus (Hu-Vir) pairwise protein-protein interaction (PPI) data
Human-Virus PPIs were retrieved from databases available on the public domain: PIG (http://pathogenportal.net/pig/) and VirusMINT (http://mint.bio.uniroma2.it/virusmint/Welcome.do), as well as few published research papers: for Vaccinia virus (Zhang et al., 2009), Dengue virus (Khadka et al., 2011), HTLV-1 and HTLV-2 (Simonis et al., 2012). Hu-Vir PPIs from aforementioned data were combined and created a non-redundant dataset after merging multiple strain/isolate specific protein identifiers (Halehalli and Nagarajaram, 2014). This dataset is available for download as tab delimited text file (hu-vir-ppi.tab).
Human-Virus Domain-Domain interactions (Hu-Vir DDIs)
Hu-Vir PPIs were scanned for Domain-Domain interactions from iPfam (ftp://selab.janelia.org/pub/ipfam) and DOMINE (http://domine.utdallas.edu/cgi-bin/Domine) and identified DDIs between human and viral protein pairs are available for download as tab delimited text file (hu-vir-ddi.txt).
Human-Virus Domain-Motif interactions (Hu-Vir DMIs)
Hu-Vir PPIs were scanned for domain and eukaryotic linear motif (ELM) interactions between human and viral proteins using linear motif binding domain (LMBD) and ELM associations in ELMdb (http://elm.eu.org/downloads.html#interactions) and predicted associations using iELM (http://i.elm.eu.org/search/). DMIs that are identified between human and viral protein pairs are available for download as tab delimited text file (hu-vir-dmi.txt).
Computational Studies on Protein – Disorder
EUMAT dataset used for eukaryotic protein's disordered region-specific amino acid substitution matrix compilation, test datasets [Less Disordered (LD), Moderately Disordered (MD) and Highly Disordered (HD)] used for homologs search performance evaluations, and EDSSMat series of matrices are available for download (Matrices and Datasets).