Target Pathogen
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Target Pathogen
metasource: Fairsharing.org
version: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Target-Pathogen
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
Target Pathogen
metasource: Fairsharing.orgversion: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Target-Pathogen
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
Target Pathogen
metasource: Fairsharing.orgversion: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Target-Pathogen
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The Target-Pathogen database is a bioinformatic approach to prioritize drug targets in pathogens. Available genomic data for pathogens has created new opportunities for drug discovery and development, including new species, resistant and multiresistant ones. However, this data must be cohesively integrated to be fully exploited and be easy to interrogate. Target-Pathogen has been designed and developed as an online resource to allow genome wide based data consolidation from diverse sources focusing on structural druggability, essentiality and metabolic role of proteins. By allowing the integration and weighting of this information, this bioinformatic tool aims to facilitate the identification and prioritization of candidate drug targets for pathogens. With the structurome and drugome information Target-Pathogen is a unique resource to analyze whole genomes of relevants pathogens.
Description
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The Target-Pathogen database is a bioinformatic approach to prioritize drug targets in pathogens. Available genomic data for pathogens has created new opportunities for drug discovery and development, including new species, resistant and multiresistant ones. However, this data must be cohesively integrated to be fully exploited and be easy to interrogate. Target-Pathogen has been designed and developed as an online resource to allow genome wide based data consolidation from diverse sources focusing on structural druggability, essentiality and metabolic role of proteins. By allowing the integration and weighting of this information, this bioinformatic tool aims to facilitate the identification and prioritization of candidate drug targets for pathogens. With the structurome and drugome information Target-Pathogen is a unique resource to analyze whole genomes of relevants pathogens.
metasource: Fairsharing.orgversion: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The successful use of antibiotics has been facing challenges because microbial pathogens are developing various forms of resistance in the last decades (1). Despite this critical situation, new drug development projects have been inadequate for reasons ranging from bad selection of targets to reduced antimicrobial drug discovery efforts by pharmaceutical companies (2, 3). Currently, it is accepted that identification and validation of appropriate targets are critical steps for designing new drugs. In this sense, Next Generation Sequencing is increasingly aiding the evaluation of gene function, essentiality and suitability for drug development. Nevertheless there is a lack of online resources that allows genome wide based data consolidation from diverse sources in order to define a list of potential targets. Here, we present Target-Pathogen database (target.sbg.qb.fcen.uba.ar/patho), an online resource that allows genome wide based target ranking and identification. By integrating and weighting the data, focusing on essentiality, metabolic role and structural druggability prediction of proteins, Target-Pathogen facilitates the identification and prioritization of candidate targets suitable for new drug development projects. Available genomic data for pathogens has created new opportunities for drug discovery and development to fight them, including new resistant and multiresistant strains. In particular structural data must be integrated with both, gene information and experimental results. In this sense, there is a lack of an online resource that allows genome wide based data consolidation from diverse sources together with thorough bioinformatic analysis that allows easy filtering and scoring for fast target selection for drug discovery. Here, we present Target-Pathogen database (http://target.sbg.qb.fcen.uba.ar/patho), designed and developed as an online resource that allows the integration and weighting of protein information such as: function, metabolic role, off-targeting, structural properties including druggability, essentiality, and omic experiments, to facilitate the identification and prioritization of candidate drug targets in pathogens. We include in the database ten genomes of some of the most relevant microorganisms for human health (Mycobacterium tuberculosis, Mycobacterium leprae, Klebsiella pneumoniae, Plasmodium vivax, Toxoplasma gondii, Leishmania major, Wolbachia bancrofti, Trypanosoma brucei, Shigella dysenteriae and Schistosoma Smanosoni) and show its applicability. New genomes can be uploaded upon request. Target-Pathogen is an easy-to-use web-based platform which allows genome wide based data consolidation from diverse sources in a user-friendly manner , with graphical interface for structural visualization and manipulation. With structurome and drugome information Target-Pathogen is a unique resource to analyze whole genomes of relevant pathogens. Using Target-Pathogen, researchers can quickly prioritize genes of interest in a fast and intuitive manner, running simple queries (such as looking for proteins with high druggability score or associated with choke-points reactions), filtering by different data, assigning numerical weights for different properties and combining these results to produce a ranked list of targets. In this sense, an aspect that distinguishes Target- Pathogen is that it permits users to upload their own data. Once the data is uploaded, it can be included to obtain a personalized ranking of candidate drug targets in pathogens. Another key feature where Target-Pathogen stands alone is its ability to rank not only proteins but entire pathways. This characteristic allows prioritizing promising pathways to develop new drugs in order to synergistically attack several proteins of the same pathway. We have now selected ten relevant genomes but the database can be easily updated with other relevant pathogens as the bioinformatic pipelines have been automatized. In this sense, we will extend Target-Pathogen to more organisms than the current version, that's why we also encourages users to request new genomes of interest and join our team by mailing to [email protected]. The goal of Target-Pathogen is not to replace wet strategies for target identification. Rather, our goal is to become a useful resource for researchers working in the field of target identification and/or drug discovery to translate biological questions in a computational tractable way by exploring, filtering and weighting the vast quantity of genome-scale data sets. Target-Pathogen will be continuously updated as part of a national initiative to develop tools for pathogens.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://target.sbg.qb.fcen.uba.ar/patho/Webpage
More detailed information about this field from each metasource.
http://target.sbg.qb.fcen.uba.ar/patho/
metasource: Fairsharing.orgversion: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://target.sbg.qb.fcen.uba.ar/patho
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
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Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens
PMID: 29106651
metasource: Fairsharing.org
version: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkx1015
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens
PMID: 29106651
metasource: Fairsharing.org
version: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkx1015
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens
PubMed citations: 20.
20 articles citing: Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens
Pathway Driven Target Selection in Klebsiella pneumoniae: Insights Into Carbapenem Exposure. PMID:35174104
Peptide-Based Vaccines for Tuberculosis. PMID:35173740
virusMED: an atlas of hotspots of viral proteins. PMID:34614039
Identification of Potential Kinase Inhibitors within the PI3K/AKT Pathway of Leishmania Species. PMID:34356660
From Genome to Drugs: New Approaches in Antimicrobial Discovery. PMID:34177572
Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. PMID:33936562
Five-year microevolution of a multidrug-resistant Mycobacterium tuberculosis strain within a patient with inadequate compliance to treatment. PMID:33926375
Carbonic Anhydrases: New Perspectives on Protein Functional Role and Inhibition in Helicobacter pylori. PMID:33815311
Combining structure and genomics to understand antimicrobial resistance. PMID:33294134
Genomics, Computational Biology and Drug Discovery for Mycobacterial Infections: Fighting the Emergence of Resistance. PMID:33101362
Prioritisation of potential drug targets against Bartonella bacilliformis by an integrative in-silico approach. PMID:32785422
Prioritization of Mur family drug targets against A. baumannii and identification of their homologous proteins through molecular phylogeny, primary sequence, and structural analysis. PMID:32725318
The Effect of Substituted Benzene-Sulfonamides and Clinically Licensed Drugs on the Catalytic Activity of CynT2, a Carbonic Anhydrase Crucial for Escherichia coli Life Cycle. PMID:32545297
A chemical inhibitor of heat shock protein 78 (HSP78) from Leishmania donovani represents a potential antileishmanial drug candidate. PMID:32471865
The antischistosomal potential of GSK-J4, an H3K27 demethylase inhibitor: insights from molecular modeling, transcriptomics and in vitro assays. PMID:32178714
Methylobacterium sp. 2A Is a Plant Growth-Promoting Rhizobacteria That Has the Potential to Improve Potato Crop Yield Under Adverse Conditions. PMID:32127795
Core regulon of the global anaerobic regulator Anr targets central metabolism functions in Pseudomonas species. PMID:31227753
Discovery and Genetic Validation of Chemotherapeutic Targets for Chagas' Disease. PMID:30666299
An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets. PMID:30018343
Draft Genome Sequence of Lactobacillus helveticus ATCC 12046. PMID:29449405 - http://dx.doi.org/10.1093/nar/gkx1015
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genome
metasource: Fairsharing.org
version: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome visualization
metasource: Fairsharing.org
version: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
pathogen
metasource: Fairsharing.org
version: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Tags
More detailed information about this field from each metasource.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome visualization
metasource: Fairsharing.orgversion: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
pathogen
metasource: Fairsharing.orgversion: FAIRsharing.org: Target Pathogen; Target Pathogen; DOI: https://doi.org/10.25504/FAIRsharing.dh32pc; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome genome visualization pathogen
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