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Host-pathogen interaction inference software tools | Pathway analysis

Can we predict protein-protein interactions (PPIs) of a novel virus with its host? Three major problems arise: the lack of known PPIs for that virus to learn from, the cost of learning about its proteins and the sequence dissimilarity among viral…
GPS-Prot
Web

GPS-Prot

A software tool that allows users to easily create an integrated human protein…

A software tool that allows users to easily create an integrated human protein network, or HIV-host networks. A major advantage of this platform compared to other visualization tools is its web-based…

DeNovo
Desktop

DeNovo

A sequence-based negative sampling and machine learning framework that learns…

A sequence-based negative sampling and machine learning framework that learns from protein-protein interactions (PPIs) of different viruses to predict for a novel one, exploiting the shared host…

bsl_mtl
Desktop

bsl_mtl Bilinear Sparse Low-rank Multitask Learning

Models interactions between human proteins and three different, but related…

Models interactions between human proteins and three different, but related viruses: Hepatitis C, Ebola virus and Influenza A. bsl_mtl uses a shared low-rank structure in addition to a task-specific…

invasive_salmon…
Desktop

invasive_salmonella

Scores the functional impact of mutations regarding to Salmonella enterica.…

Scores the functional impact of mutations regarding to Salmonella enterica. invasive_salmonella allows detection of patterns of gene degradation associated with invasiveness in Salmonella. It is…

LRLSHMDA
Algorithm
Hi-Jack
Desktop

Hi-Jack

A computational framework for inferring pathway-based interactions between a…

A computational framework for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking. Hi-Jack searches metabolic network data from hosts…

HPIA
Desktop

HPIA Host-Pathogen Interaction Alignment

An algorithm that can be used to identify common sets of host-pathogen…

An algorithm that can be used to identify common sets of host-pathogen interactions by aligning (mapping) host-to-host and pathogen-to-pathogen proteins from two interaction datasets. HPIA algorithm…

BioAfrica
Dataset

BioAfrica

Provides information on Human Immunodeficiency Virus (HIV) proteins. BioAfrica…

Provides information on Human Immunodeficiency Virus (HIV) proteins. BioAfrica is a resource collaborating with Swiss-Prot ViralZone group of the Swiss Institute of Bioinformatics (SIB). The database…

CAPIH
Web

CAPIH Comparative Analysis of Protein Interactions for HIV-1

Provides comparative information between human and the three model organisms in…

Provides comparative information between human and the three model organisms in the context of host-HIV-1 protein interactions. CAPIH identifies genetic changes that occur in HIV-1-interacting host…

InterSPPI
Web
Desktop

InterSPPI Inter-Species Protein–Protein Interaction predictor

Allows prediction of plant–pathogen protein–protein interaction. InterSPPI…

Allows prediction of plant–pathogen protein–protein interaction. InterSPPI is a webserver, implementing a Random Forest (RF)-based method, that was developed to predict Arabidopsis–pathogen…

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