RNAapt3D is a database of RNA aptamer which contains RNA sequences, their secondary/tertiary structural information, target proteins of RNA aptamers and network of RNA-protein interaction. The tertiary structures are predicted by a given RNA sequence considering a wide variety of secondary structures with a modelling tool, RASCAL, and molecular dynamics simulations. This database can be used to provide insights for tertiary structural analysis, motif search with base flip position and a starting point by RNA-protein complex molecular simulations.
This database facilitates a study on the design of RNA aptamer for a target molecule and improves the efficiency and the productivity in candidate selection.


Ryuma Sato, Koji Suzuki, Yuichi Yasuda, Atsushi Suenaga, Kazuhiko Fukui, "RNAapt3D: RNA aptamer 3D-structural modeling database", Biophys J. 2022 Sep 22;S0006-3495(22)00773-1.
PMID: 36146935   DOI: 10.1016/j.bpj.2022.09.023