Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments
Open accessAbstract
Over the past several decades, rapid developments in both molecular and information technology have collectively increased our ability to understand molecular recognition. One emerging area of interest in molecular recognition research includes the isolation of aptamers. Aptamers are single-stranded nucleic acid or amino acid polymers that recognize and bind to targets with high affinity and selectivity. While research has focused on collecting aptamers and their interactions, most of the information regarding experimental methods remains in the unstructured and textual format of peer reviewed publications. To address this, we present the Aptamer Base, a database that provides detailed, structured information about the experimental conditions under which aptamers were selected and their binding affinity quantified. The open collaborative nature of the Aptamer Base provides the community with a unique resource that can be updated and curated in a decentralized manner, thereby accommodating the ever evolving field of aptamer research. DATABASE URL: http://aptamer.freebase.com.
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High-affinity aptamers recognize more than 900 different targets.
“At present, high-affinity aptamers recognize more than 900 different targets, including cytokines, growth factors, proteases, immunoglobulins, cell surface receptors, and cell adhesion molecules.240,241”
From Smart nanoparticles for cancer therapy (2023) · cites this paper as [240]
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- Authors
- Cruz-Toledo, J., McKeague, M., Zhang, X., Giamberardino, A., McConnell, E., Francis, T., DeRosa, M. C., & Dumontier, M.
- Affiliations
- Department of Biology, Carleton University, 2Department of Chemistry, Carleton University, 3Institute of Biochemistry, Department of Biology and Department Chemistry, Carleton University and 4School of Computer Science, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
- Carleton University (CA)
- Corresponding author
- McKeague, Maureen
- DeRosa, Maria C.
- Dumontier, Michel
- Venue
- Database
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-01-01
- Volume
- 2012
- Pages
- bas006-bas006
- ISSN
- 1758-0463 (ISSN-L)
- PMC
- PMC3308162
- OpenAlex
- W2135504399
- Cited by
- 95
- References
- 39
- Citations by year
- 2026: 7 · 2025: 8 · 2024: 5 · 2023: 10 · 2022: 4 · 2021: 5 · 2020: 6 · 2019: 4 · 2018: 4 · 2017: 6 · 2016: 12 · 2015: 6 · 2014: 7 · 2013: 7 · 2012: 4
- FWCI
- 3.08
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Database (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research Publications (Maastricht University) (acceptedVersion, cc-by-nc)
- Carleton University's Institutional Repository (MacOdrum Library, Carleton University) (submittedVersion, other-oa)
- Research Publications (Maastricht University) (submittedVersion, cc-by-nc)
- Funders
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- aptamers, SELEX, aptamer selection, knowledge base, binding affinity, molecular recognition, protein-nucleic acid interactions, data curation
- MeSH terms
- Database Management Systems, Research Design, Databases, Factual, SELEX Aptamer Technique, Aptamers, Nucleotide, Aptamers, Peptide
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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