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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…

WDNfinder
Desktop

WDNfinder

Provides structural controllability with consideration of node connection…

Provides structural controllability with consideration of node connection strength in biological networks. WDNfinder is composed of two algorithms: (1) maximum weight MDS (MWMDS) identification, (2)…

SalmoNet
Dataset

SalmoNet

Gathers network data (metabolic, regulatory, protein-protein interaction) for…

Gathers network data (metabolic, regulatory, protein-protein interaction) for 10 representative pathogenic Salmonella strains. SalmoNet is an online database regrouping information on interactions…

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

LRLSHMDA Laplacian Regularized Least Squares for Human Microbe–Disease Association

Provides a computational model for deducing the most potential human…

Provides a computational model for deducing the most potential human microbe-disease association. LRLSHMDA introduces Gaussian interaction profile kernel similarity and Laplacian regularized least…

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…

PREMER
Desktop

PREMER Paralell Reverse Engineering with Mutual information & Entropy Reduction

Allows users to recover and determine the strength and causality of…

Allows users to recover and determine the strength and causality of interactions. PREMER allows incorporation of prior knowledge, imputation of missing data, and correction of outliers. This tool is…

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…

PPIN
Web

PPIN Plant-Pathogen Immune Network

Allows exploration of the Plant-Pathogen Immune Network. PPIN includes more…

Allows exploration of the Plant-Pathogen Immune Network. PPIN includes more than 3000 interactions among about 900 immune related proteins. Of these 900 immune related proteins we count over 80…

InterSPPI
Web
Desktop

InterSPPI Inter-Species Protein–Protein Interaction predictor

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

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…

HoPItor
Web

HoPItor

Assists users for protein interaction. HoPItor is a web app that provides a…

Assists users for protein interaction. HoPItor is a web app that provides a host-pathogen protein interaction prediction.

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