AliasesRNA aptamer 3D-structural modeling database
DescriptionRNAapt3D 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.
Main Institutes of managementNational Institute of Advanced Industrial Science and Technology (AIST)
Country of the InstituteJapan
URL of the site
Input exampleYou can search RNA sequence in RNA apt3D database. Click on the “Search” at the top. Enter the RNA sequence in Motif Search, where the input sequence can be in upper or lower case. If you click “Sample” button, an example sequence will be entered. Click on the “Search” button, Motif search will take a few tens of seconds. Some entries containing a given RNA sequence and the predicted base flip positions for these entries will be displayed. Search result can be downloaded by clicking download icon.
KeywordRNA aptamer | drug
Amount of the all data for download(Mbyte) | Method to obtain the all data.0.0|none
External resources (databases) in building the product.None
Data typeRNA structure
Biological species in the main concernNone
Conditions of useNone
Frequency of updates (in last two years)any time
Last date of updates (date of confirmation)2022/09/22(2022/11/16)
Main IDs used in the productsMedals oligonucleic drug ID
How to make a link to get access to each IDs.None
external databases to which this database/tool have linksNone
Published papers (PubMed IDs)PMID:36146935
Operational Statusavailable