ArticleBMC bioinformatics2006
RiboaptDB: a comprehensive database of ribozymes and aptamers.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 34 citations in OpenAlex.
- In vitro selection of aptamers and their applications.Nature reviews. Methods primers · 2023Article
- AptaNet as a deep learning approach for aptamer-protein interaction prediction.Scientific reports · 2021Article
- Analysis of In Vitro Aptamer Selection Parameters.Journal of molecular evolution · 2015Review
- Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments.Database : the journal of biological databases and curation · 2012Article
- Computational approaches toward the design of pools for the in vitro selection of complex aptamers.RNA (New York, N.Y.) · 2010Article
- Simple fluorescent sensors engineered with catalytic DNA 'MgZ' based on a non-classic allosteric design.PloS one · 2007Article
- Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.BMC bioinformatics · 2007Article
- Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction.BMC bioinformatics · 2006Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundCatalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selected oligo-nucleotide sequences (~200 bp in length) have the ability to recognize broad range of specific ligands by forming binding pockets. These novel aptamer sequences can bind to nucleic acids, proteins or small organic and inorganic chemical compounds and have many potential uses in medicine and technology.
resultsThe comprehensive sequence information on aptamers and ribozymes that have been generated by in vitro selection methods are included in this RiboaptDB database. Such types of unnatural data generated by in vitro methods are not available in the public 'natural' sequence databases such as GenBank and EMBL. The amount of sequence data generated by in vitro selection experiments has been accumulating exponentially. There are 370 artificial ribozyme sequences and 3842 aptamer sequences in the total 4212 sequences from 423 citations in this RiboaptDB. We included general search feature, and individual feature wise search, user submission form for new data through online and also local BLAST search.
conclusionThis database, besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility in medicine, provides valuable information for computational and theoretical biologists. The RiboaptDB is extremely useful for garnering information about in vitro selection experiments as a whole and for better understanding the distribution of functional nucleic acids in sequence space. The database is updated regularly and is publicly available at http://mfgn.usm.edu/ebl/riboapt/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.