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. 2024 Feb 16;30(3):189-199.
doi: 10.1261/rna.079784.123.

AptaDB: a comprehensive database integrating aptamer-target interactions

Long Chen #  1 , Zhuohang Yu #  1 , Zengrui Wu  1 , Moran Zhou  1 , Yimeng Wang  1 , Xinxin Yu  1 , Weihua Li  1 , Guixia Liu  1 , Yun Tang  2
Affiliations

AptaDB: a comprehensive database integrating aptamer-target interactions

Long Chen et al. RNA. .

Abstract

Aptamers have emerged as research hotspots of the next generation due to excellent performance benefits and application potentials in pharmacology, medicine, and analytical chemistry. Despite the numerous aptamer investigations, the lack of comprehensive data integration has hindered the development of computational methods for aptamers and the reuse of aptamers. A public access database named AptaDB, derived from experimentally validated data manually collected from the literature, was hence developed, integrating comprehensive aptamer-related data, which include six key components: (i) experimentally validated aptamer-target interaction information, (ii) aptamer property information, (iii) structure information of aptamer, (iv) target information, (v) experimental activity information, and (vi) algorithmically calculated similar aptamers. AptaDB currently contains 1350 experimentally validated aptamer-target interactions, 1230 binding affinity constants, 1293 aptamer sequences, and more. Compared to other aptamer databases, it contains twice the number of entries found in available databases. The collection and integration of the above information categories is unique among available aptamer databases and provides a user-friendly interface. AptaDB will also be continuously updated as aptamer research evolves. We expect that AptaDB will become a powerful source for aptamer rational design and a valuable tool for aptamer screening in the future. For access to AptaDB, please visit http://lmmd.ecust.edu.cn/aptadb/.

Keywords: annotation; aptamer–target interaction; database; similar aptamers.

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Figures

FIGURE 1.
FIGURE 1.
An overview of the different modules and features provided by AptaDB. Its main input and output data are shown in different colors.
FIGURE 2.
FIGURE 2.
Statistics of AptaDB. (A) Percentage of RNA and ssDNA (inner circles) and percentage of different aptamer–target interactions (outer circles). (B) Distribution of affinity between aptamer and targets in AptaDB. (C) Distribution of RNA aptamer length. (D) Distribution of DNA aptamer length. (E) Distribution of aptamers with different numbers of G-quadruplex (prediction by QGRS mapper). (F) Distribution of the number of different aptamer functions. (G) Relationship between aptamer length and affinity. The affinity values have been logarithmically transformed using the formula log(affinity + 1) for smoother representation. (H) Relationship between GC content and affinity. The affinity values have been logarithmically transformed using the formula log(affinity + 1) for smoother representation.
FIGURE 3.
FIGURE 3.
Homepage, search and browse pages of AptaDB. (A) The main interface includes a description of the database and “Search” access. (B) Introduction of aptamer and SELEX and statistical information of AptaDB. (C) The search interface provides text and structure-based input to query for aptamer–target interaction. (D) Data browsing. (E) Structure-based similarity search by drawing structures.
FIGURE 4.
FIGURE 4.
Six components of AptaDB. (A) Aptamer–target interaction information. (B) Structure information of aptamer. (C) Aptamer information. (D) Target information. (E) Activity data. (F) Similar aptamers.
FIGURE 5.
FIGURE 5.
The basic data collection, processing phases, data classification, and data presentation of AptaDB.
See this image and copyright information in PMC

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