AptBacterialDB: A Comprehensive, Manually Curated Database of Antibacterial Aptamers

Abstract

In recent years, aptamers have transitioned from mere laboratory tools to highly potent molecular recognition agents capable of overcoming the strict limitations of conventional antibiotic therapies. We have developed AptBacterialDB, a manually curated, large, comprehensive database of experimentally validated antibacterial aptamers spanning 1996 to 2026. The database contains a total of 2131 aptamers targeting approx 75 different bacterial classes, and 124 aptamer targets with 95 entries found in UTexas databases, 97 in AptaDB, and 28 in Aptabase. It contains 1555 unique aptamer sequences, 189 unique modifications, 40 different selection approaches, and 44 different affinity methods. It integrates detailed annotations of about 20 fields, including sequence information, nucleic acid type, binding affinity, modifications, experimental and functional details. The secondary structure of the aptamers was predicted using ViennaRNA Package 2.0, demonstrating that they adopt mostly stable conformations, with a structured stem region. MySQL was implemented for database development, and a knowledge graph was integrated using ArcadeDB/openCypher for graphical visualization of aptamer-target-organisation relationships. Facilities such as different search modes, browsing, similarity search, REST API access, and entries linked to the existing database for a broader view of the aptamers have been provided. AptBacterialDB (https://webs.iiitd.edu.in/raghava/aptbacterialdb/) provides a user-friendly centralized platform to accelerate antibacterial aptamer research, therapeutic development, biosensor design, and computational modelling efforts. Authors BiographyO_LINisha Bajiya is currently working as Ph.D. Student in Computational Biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LIO_LIIshika Gupta is currently working as an M.Tech Student in Computational Biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LIO_LIGajendra P. S. Raghava is currently working as a Professor in the Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India C_LI