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PHI-base / Pathogen-Host Interactions database
Catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. It proposes improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. PHI-base contains information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions.
VirHostNet / Virus-Host Network
Supplies a collection of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. VirHostNet simplifies systems biology and gene-centered analysis of infectious diseases and assists users in the recognition of new molecular targets for antiviral drugs design. It aims to improve the knowledge on molecular mechanisms involved in the antiviral response mediated by the cell and in the viral strategies selected by viruses to hijack the host immune system.
HoPaCI-DB / Host-Pseudomonas and Coxiella Interaction DataBase
A manually curated database of interactions between host-pathogen-related elements such as biomolecules (proteins, metabolites etc.) and other factors (biological processes, cellular components etc.). HoPaCI-DB is an analysis resource for the study of the pathogens Pseudomonas aeruginosa and Coxiella species. The majority of host species refers to mammalia, but also results from experiments with C. elegans, Drosophila melanogaster or Danio rerio are included. The aim of HoPaCI-DB is to serve as knowledge base for experimentally- oriented scientists and as resource for bioinformatics applications.
HIV-1 Human Interaction Database
Provides a database of known interactions of HIV-1 proteins with proteins from human hosts. HIV-1 Human Interaction Database is an online resource that includes annotated bibliographies of published reports of protein interactions, with links to the corresponding PubMed records and sequence data. It also integrates published reports of two types of interactions - protein interactions, and human gene knock-downs that affect virus replication and infectivity.
Facilitates both the identification and functional analysis of host–pathogen interactions (HPI) for a broad range of pathogens and their hosts. HPIDB 2.0 provides targeted curation, integration with existing HPI data from external sources and tool(s) to predict additional HPI where annotated data is scarce. This unique quality of HPIDB 2.0 ensures that researchers have access to the most comprehensive data set for their system and avoid the time-consuming series of steps required to integrate, standardize and annotate HPI data.
PHISTO / pathogen-host interaction search tool
Provides pathogen–host interactions (PHIs) information. PHISTO is a web-accessible platform allowing to access to PHI data for all pathogen types. The database is updating each month in order to give access to users to up-to-date PHI data. It contains several functions which permit: (1) visualization of PHI network, (2) graph–theoretical analysis of targeted human proteins, (3) BLAST search and text mining for spotting new experimental methods.
HMDAD / human microbe–disease association database
Allows researchers and scientists to find knowledge and clinical solutions for disease mechanism understanding, diagnosis and therapy. HMDAD is a database based on microbiota studies in order to collect the human microbe-disease association data. The web interface of the database has a browse mode, a search mode, and permits users to download the dataset. It integrates more than 480 disease-microbe entries including about 30 diseases and 290 microbes.
PPIRA / Protein Protein Interactions between Ralstonia solanacearum and Arabidopsis thaliana
A database on protein-protein interactions between ralstonia solanacearum (a plant pathogen) and arabidopsis thaliana (its host). Using two computational methods, the interolog and the domain-based methods, we predicted 3,074 potential PPIs between 119 R. solanacearum and 1,442 A. thaliana proteins. Interestingly, we found that the potential pathogen-targeted proteins are more important in the A. thaliana PPI network.
EWET-DB / EmsB Website for Echinococcus Typing – DataBase
Records, shares and provides access to data about E. multilocularis, focusing on the EmsB microsatellite. EWET-DB consists in a reference collection dedicated to Echinococcus genetic data. Users can consult isolate data (including EmsB data) and distribution map from the database using different criteria (host, country, province, year of sampling, etc.). The database also allows researchers to perform genetic and spatial analyses on the reference collection and their own data.
Gathers network data (metabolic, regulatory, protein-protein interaction) for 10 representative pathogenic Salmonella strains. SalmoNet is an online database regrouping information on interactions from multiple layers of biological organization. This repository allows users to study pathogen Salmonella with details in a standardized and documented format. It can be applied by medical microbiologists and epidemiologists to understand the strain specific differences of Salmonella.
OrthoHPI / Orthology–based Host–parasite Protein–protein Interactions
Unravels the host–parasite interactome across 12 human parasites. OrthoHPI is based on orthology and its strengths. This tool (1) incorporates high–confidence intra–species interactions, (2) uses fined grained orthology assignments instead of simple sequence similarity and (3) includes parasite–specific biological context. The platform can be useful in parasites genomics, considering that a large number of parasite´s proteins are annotated as hypothetical proteins, it provides a useful resource for annotation of those proteins.
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 provides webpages divided into six sections. These are: (i) General Overview, (ii) Protein Function and Host–Virus Protein Interactions, (iii) Genomic Location and Protein Sequence, (iv) Protein Domains/Folds/Motifs, (v) HIV antiretrovirals (ARVs) and Drug Resistance Mutations and (vi) Primary and Secondary Database Entries.
Host pathogen interactomes
Hosts pathogens implicated in many human diseases, like Herpes simplex and Alzheimer's disease, the Epstein-Barr virus and multiple sclerosis or Chlamydia pneumoniae and atherosclerosis. The host pathogen interactomes database assembles Bornavirus, Borrelia Burgdorferi, Candida albicans, Chlamydia Pneumoniae, Cryptococcus Neoformans, Ebola virus, Epstein-Barr virus, Helicobacter pylori, Hepatitis C virus, Herpes simplex (HSV-1), HERV-W, Human cytomegalovirus, Influenza A virus, Porphyromonas Gingivalis, Toxoplasma Gondii, Trypanosoma Cruzi. These interactomes can also be accessed here and links to other interactome sites are also provided.
EHFPI / Essential Host Factors for Pathogenic Infection
A database of Essential Host Factors (EHFs) for Pathogenic Infections. This database focuses on the collection and functional analysis of a specialized class of host cellular genes identified from (genome-wide) RNA interface (RNAi) screens. Notably, the knockdown effect of these genes greatly influences the infection of a pathogen (e.g., inhibit or increase infection) but not the viability of the host cells, thus designated as essential host factors (EHFs) for pathogenic infections.
Aims at collecting and annotating in a structured format all the interactions between human and viral proteins and to integrate this information in the human protein interaction network. The curation effort has focused on manuscripts reporting interactions between human proteins and proteins encoded by some of the most medically relevant viruses: papilloma viruses, human immunodeficiency virus 1, Epstein-Barr virus, hepatitis B virus, hepatitis C virus, herpes viruses and Simian virus 40.
An open and free public database server for protein interaction information for Xanthomonas oryzae pathovar oryzae (Xoo). It contains 4,538 proteins and 26,932 possible interactions consisting of 18,503 (PSIMAP), 3,118 (PEIMAP), and 8,938 (iPfam) pairs. In addition, XooNET provides 3,407 possible interaction pairs between two sets of proteins; 141 Xoo proteins that are predicted as membrane proteins and rice proteomes. The resultant interacting partners of a query protein can be easily retrieved by users as well as the interaction networks in graphical web interfaces.
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