User Guide
Version 1.2
2022/8/12

Contents
1

Introduction _______________________________________________________2

2

Querying the Database ______________________________________________3
2.1

Search of information of Model __________________________________ 3

2.2

Search for RNA motif ___________________________________________ 8

3Interaction _______________________________________________________104

Statistics _________________________________________________________12

5

Contact Us _______________________________________________________14

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1 Introduction
RNAapt3D 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. This datab ase 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.
RNAapt3D lets you creatively promote on your project for the development ofnew RNA aptamer.

22 Querying the Database
2.1 Search of information of Model
Menu items are shown at the top of RNAapt3D page.

A)A) Browser aptamer models
Click on the “Model” at the top menu, you can browser the RNA sequence, thetarget protein, and the structural information of each entry (monad’s ID).

D)B)

C)

3B) View detail information of RNA aptamer
Click on the “monad’s ID” (for example: monad0015) in the list, the detail ofits RNA aptamer will be shown.

DownloadTertiary structure model PDB file can be downloaded by clicking icons beside modellinks.

4C) Inspec target protein
Click on the “Target protein’s name” (for example: PDGF-B) in the list, thenUniprot page related to its protein will open in new window. Confirm the detailof its protein.

5D) View tertiary structure
Click on the “Model”, “Opt. Model”, or “Mod. Model” at the right tertiary
structure section. PDBe Mol* Viewer page will open in new window.
“Model” structure was predicted by Rascal. “Opt. Model” and “Mod. Model”
structures were relaxed by MD simulations for Rascal model structure within
Na + solute respectively. MD simulations from 5 to 10 ns were classified into
10 clusters according to their structural similarities using a k -means method.
Ten representative structures for each cluster are stored as the optimized model.

The tertiary structure can be directly confirmed.

6Click on the specific nucleotide on this viewer. Some interactions between its
nucleotide and other nucleotides can be confirmed.

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2.2 Search for RNA motif
You can search RNA sequence in RNAapt3D database.

A)A) Navigate to search page
Click on the “Search” at the top.

B)C)B) Enter the RNA sequence
Enter the RNA sequence in Motif Search, where the input sequence can be inupper or lower case. If you click “Sample” button, an example sequence willbe entered.

8C) Execute Search
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.

Download

Search result can be downloaded by clicking download icon.

93 Interaction
You can check interactions between aptamer and protein, and betwe en protein
and protein.

A)A) Move to interaction page
Click on the “Interaction” at the top menu.

10It shows RNA aptamer (orange square)-Target proteins (blue square)interactions. The proteins (green square) connected to the target proteins (bluesquare) are obtained by projecting on protein-protein interaction network ofHuman Protein Reference Database.

The + and- signs in the upper right zoom in and out of the network diagram.

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4 Statistics
Statistical information is on Statistics page.

A)A) Move to statistics page
Click on the “Statistics” at the top.

The number of RNA aptamer included this database for each clinical phase canbe confirmed.

12Following shows legend for this chart.

Clinical Trial Phase
ADApproved Drug

II/III

Phase II/IIIIII

Phase IIIPC

Pre-Clinical Phase13

5 Contact Us
RNAapt3D
URL: https://rnaapt3d.medals.jp

If you have any questions or comments, please contact the following e -mailaddress.
mail: k-fukui (+@aist.go.jp)

Acknowledgments:
This research was supported in part by the Life-Science Database Integration
Project at the Japan Science and Technology Agency (JST).

Cellular and Molecular Biotechnology Research Institute (CMBRI) ,National Institute of Advanced Industrial Science and Technology (AIST) ,Tokyo Waterfront Bio-IT Research Building 2-4-7 Aomi,
Koto-ku,Tokyo,135-0064, Japan

Copyright ©CMBRI, AIST, 2022 All Rights Reserved.

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