97
Table 4.4 Host interaction and metabolic network reconstruction – databases and tools
Database/tool
Content
Website
Reference
Pathogen Host Interaction (PHI) It provides curated biological and molecular information on genes
affecting pathogen-host interactions.
http://www.phi-base.org/
Urban et al.
(2017)
Host-Pathogen Interaction
Database – (HPIDB 3.0)
Containing 69,441 curated entries, providing annotation, prediction,
and display of host-pathogen interactions (HPI)
http://hpidb.igbb.msstate.edu/
Ammari et al.
(2016)
Pathogen-Host Interaction
Search Tool (PHISTO)
It provides data for all pathogen types with experimentally verified
protein interactions with the human host
http://www.phisto.org/
Durmus Tekir
et al. (2013)
Host-Pathogen and Coxiella
Interaction database
(HoPaCI-db)
A manually curated database of interactions between hostpathogen- related elements and other factors from Pseudomonas
aeruginosa and Coxiella species.
http://mips.helmholtz-muenchen.
de/HoPaCI/
Bleves et al.
(2014)
Pathogen-host interaction data
integration and analysis system
(PHIDIAS)
It is a database and analysis system that aims to manually curate,
computationally analyse pathogen-host interactions
http://www.phidias.us/
Xiang et al.
(2007)
VirHostNet
Includes almost 35.000 virus-host and virus-virus manually curated
protein-protein interactions
http://virhostnet.prabi.fr/
Guirimand et al.
(2015)
VirusMentha
Contains more than 5000 proteins and almost 16.000 host-virus
protein interactions
https://virusmentha.uniroma2.it/ Calderone et al.
(2015)
HCVpro
It is a database of Hepatitis C Virus (HCV) protein interactions and
provides molecular data, functional annotations, drug development,
pathways links to other biological databases.
http://www.cbrc.kaust.edu.sa/
hcvpro/
Kwofie et al.
(2011)
CarveMe
Genome-scale metabolic model reconstruction
https://pypi.org/project/carveme/ Machado et al.
(2018)
Integrated pathway gene
relationship database (IntPath)
Database with information from S. cerevisiae, M. tuberculosis
H37Rv, H. Sapiens,
and M. musculus
https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC3521174/
Zhou et al.
(2012)
Kegg Pathway Database
Provides network and pathway maps
https://www.genome.jp/kegg/
pathway.html
Kanehisa et al.
(2008)
(continued)
4 In Silico Approaches for Prioritizing Drug Targets in Pathogens
Table 4.4 Host interaction and metabolic network reconstruction – databases and tools
Database/tool
Content
Website
Reference
Pathogen Host Interaction (PHI) It provides curated biological and molecular information on genes
affecting pathogen-host interactions.
http://www.phi-base.org/
Urban et al.
(2017)
Host-Pathogen Interaction
Database – (HPIDB 3.0)
Containing 69,441 curated entries, providing annotation, prediction,
and display of host-pathogen interactions (HPI)
http://hpidb.igbb.msstate.edu/
Ammari et al.
(2016)
Pathogen-Host Interaction
Search Tool (PHISTO)
It provides data for all pathogen types with experimentally verified
protein interactions with the human host
http://www.phisto.org/
Durmus Tekir
et al. (2013)
Host-Pathogen and Coxiella
Interaction database
(HoPaCI-db)
A manually curated database of interactions between hostpathogen- related elements and other factors from Pseudomonas
aeruginosa and Coxiella species.
http://mips.helmholtz-muenchen.
de/HoPaCI/
Bleves et al.
(2014)
Pathogen-host interaction data
integration and analysis system
(PHIDIAS)
It is a database and analysis system that aims to manually curate,
computationally analyse pathogen-host interactions
http://www.phidias.us/
Xiang et al.
(2007)
VirHostNet
Includes almost 35.000 virus-host and virus-virus manually curated
protein-protein interactions
http://virhostnet.prabi.fr/
Guirimand et al.
(2015)
VirusMentha
Contains more than 5000 proteins and almost 16.000 host-virus
protein interactions
https://virusmentha.uniroma2.it/ Calderone et al.
(2015)
HCVpro
It is a database of Hepatitis C Virus (HCV) protein interactions and
provides molecular data, functional annotations, drug development,
pathways links to other biological databases.
http://www.cbrc.kaust.edu.sa/
hcvpro/
Kwofie et al.
(2011)
CarveMe
Genome-scale metabolic model reconstruction
https://pypi.org/project/carveme/ Machado et al.
(2018)
Integrated pathway gene
relationship database (IntPath)
Database with information from S. cerevisiae, M. tuberculosis
H37Rv, H. Sapiens,
and M. musculus
https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC3521174/
Zhou et al.
(2012)
Kegg Pathway Database
Provides network and pathway maps
https://www.genome.jp/kegg/
pathway.html
Kanehisa et al.
(2008)
(continued)
4 In Silico Approaches for Prioritizing Drug Targets in Pathogens