CMsiRNAdb: a database of chemically modified SiRNA silencing efficiency for nucleic acid drug design

BACKGROUND: Small interfering RNA (siRNA) is a powerful tool for gene silencing, but its clinical application is limited by instability and potential immunogenicity. While chemical modification is essential to overcome these hurdles, data on chemically modified siRNAs are currently scattered, hindering rational drug design and development. RESULTS: We developed CMsiRNAdb, a comprehensive database integrating data resources, analytical tools, and efficacy prediction for chemically modified siRNAs. We consolidated 43,153 experimentally validated sequences and silencing efficiency data derived from 90 patents, covering 36 modification types and 13 therapeutic target genes. The database offers multi-dimensional retrieval, visualization, and batch download functions. Furthermore, we developed ModMapper, a Trie tree-based tool for precise identification of modification sites, and integrated the Cm-siRPred model for efficacy evaluation. CMsiRNAdb is freely accessible at https://cellknowledge.com.cn/CMsiRNAdb/ . CONCLUSION: CMsiRNAdb provides critical data support and analytical tools for the rational design and rapid optimization of siRNA drugs. By standardizing data and offering predictive capabilities, it significantly advances the development of nucleic acid therapeutics.