Databases
R-SIM (RNA-Small molecule Interaction Miner) is a database of 2501 experimentally validated RNA-small molecule interactions curated from existing databases and literature. It includes binding affinity values (in molar units), experimental conditions from literature, several types of RNA-specific and small molecule-specific information, experimental or modelled complex structures, and the reference article for each interaction. It is maintained by the Protein Bioinformatics Lab at Indian Institute of Technology, Madras, India.
SMMRNA is a database of ~1000 experimentally verified RNA-small molecule interactions curated from literature. It includes data on secondary structure of RNA target, molecular graph of the small molecule, binding affinity values (in micromolar units) and the reference article for each interaction.
R-BIND was compiled to analyze the distinct features of RNA chemical probes for the rational design of RNA-biased screening libraries. The database includes ~250 RNA-active small molecules (SM) and multi-valent ligands (MV). The database is maintained by the Hargrove lab at Duke University, North Carolina and is updated biennially.
NALDB (Nucleic Acid-Ligand DataBase) is a database of nucleic acid-ligand interactions including both DNA- and RNA-small molecule interactions. Nucleic acid targets are divided into 5 sub-categories: G-quadruplex DNA, G-quadruplex RNA, Double stranded DNA, Double stranded RNA and Special structure nucleic acid. It is maintained by the Indian Institute of Technology, Indore, India.
ROBIN (Repository Of nucleic acid BINders) is a dataset compiled from small molecule microarray (SMM) screening studies involving 36 nucleic acid targets and 24,572 small molecules. The data includes 3D structures of all small molecules (in SDF format), sequences of the RNA targets involved and binary labels indicating whether the molecule is active or inactive for every RNA target considered. A machine learning-based classification model constructed with the dataset has also been open-sourced in the adjoined preprint. The repository is maintained by the Chemical Biology Laboratory at NCI, NIH.
NoncoRNA is a database of experimentally verified non-coding RNAs and drug targets in cancer. The current version of the database contains 5,568 non-coding RNAs and 154 drugs spanning 134 cancer types. However, the binding affinity information is not provided for RNA-drug interactions. It is maintained by the Harbin Medical University, China.
Web servers
Inforna is a popular web server for sequence-based prediction of potential RNA-small molecule interactions. It utilizes a curated database of RNA motif-small molecule interactions as the knowledgebase for predictions and has been validated extensively in multiple studies. It is maintained by the Disney lab at The Scripps Research Institute, Florida.
RNAmigos is a server for RNA secondary structure graph-based prediction of small molecules. The method can also take as input a library of small molecules and screen it against a given RNA graph to identify potential hits. It works based on a pre-trained deep learning model to extract features similar to existing RNA-small molecule complexes. It is maintained by McGill University, Canada.
RNALigands is a server for RNA motif search-based prediction of small molecules. The method utilizes a curated database of RNA motif-small molecule interactions from PDB, Inforna and R-BIND to predict molecules for a given RNA sequence. It is maintained by the Zhang lab and Yang lab at the University of Toronto, Canada.
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