Pharos 2023: an integrated resource for the understudied human proteome
Open accessAbstract
The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for users to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts.
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Combined with AI-based protein structure prediction systems such as AlphaFold and RoseTTafold, these resources are poised to accelerate AI4DD.
“Combined with AI-based systems that predict protein structures, such as AlphaFold (23) and RoseTTafold (24), these resources are poised to accelerate AI4DD.”
From Artificial Intelligence for Drug Discovery: Are We There Yet? (2024) · cites this paper as [23]
The Results (Target details pages; page unavailable) say Pharos includes predicted protein structures from AlphaFold, and the Abstract describes using Pharos to address drug-discovery questions. The paper does not say that combining these resources with protein-structure prediction systems will accelerate AI4DD; that forward-looking conclusion goes beyond what it reports. (LLM, conf=0.83)
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Informatic challenges and advances in illuminating the druggable proteome
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Chemical coverage of human biological pathways
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Spike-In Proteome Enhances Data-Independent Acquisition for Thermal Proteome Profiling
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A general assay platform to study protein pharmacology using ligand-dependent structural dynamics
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Genetic evidence informs the direction of therapeutic modulation in drug development
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Chemistry and Technology Innovation to Advance Green and Sustainable Chemistry
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A ligand-receptor interactome of the bone tumor microenvironment in multiple myeloma bone pain
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Self-citationIdentifying and Filling the Chemobiological Gaps of Gut Microbial Metabolites
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Computational Drug Repositioning in Cardiorenal Disease: Opportunities, Challenges, and Approaches
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TARRAGON: Therapeutic Target Applicability Ranking and Retrieval-Augmented Generation Over NetworksPreprint
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Probe my Pathway (PmP): a portal to explore the chemical coverage of the human Reactome
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Identifying prognostic targets in metastatic prostate cancer beyond AR
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Computational Drug Repurposing
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Beyond the streetlight: a TREAT‐AD perspective on where to find new Alzheimer's targets
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- Authors
- Kelleher, K. J., Sheils, T. K., Mathias, S. L., Yang, J. J., Metzger, V. T., Siramshetty, V. B., Nguyen, D.-T., Jensen, L. J., Vidović, D., Schürer, S. C., Holmes, J., Sharma, K. R., Pillai, A., Bologa, C. G., Edwards, J. S., Mathé, E. A., & Oprea, T. I.
- Affiliations
- National Center for Advancing Translational Sciences (US)
- University of New Mexico (US)
- National Center for Advancing Translational Science , 9800 Medical Center Drive , Rockville , MD 20850, USA
- University of Copenhagen (DK)
- University of Miami (US)
- Corresponding author
- Edwards, Jeremy S
- Mathé, Ewy A
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-11-29
- Volume
- 51
- Issue
- D1
- Pages
- D1405-D1416
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC9825581
- OpenAlex
- W4310240482
- Cited by
- 137
- References
- 51
- Citations by year
- 2026: 39 · 2025: 42 · 2024: 46 · 2023: 10
- FWCI
- 13.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc)
- Funders
- National Institutes of Health (U24 CA224370, U24 TR002278)
- Novo Nordisk Foundation (NNF14CC0001)
- Intramural Research Program, NCATS
- Intramural/Extramural research program of the NCATS, NIH: Knowledge Management Center for Illuminating the Druggable Genome (ZIA TR000057-08)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Keywords
- Pharo, human proteome, disease biology, drug discovery, small molecule perturbations
- MeSH terms
- Biological Products, Humans, Databases, Factual, Internet, Proteome, Drug Discovery, Molecular Targeted Therapy
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