FR3D project page

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FR3D Basepair catalog | FR3D Base-phosphate interactions | FR3D motif library | BGSU RNA group home page

New! Try WebFR3D, the online version of FR3D.
New! Try R3D Align to align RNA 3D structures.

FR3D stands for "Find RNA 3D" and is commonly pronounced "Fred".  It was developed to find small RNA motifs (two to 20 nucleotides) in PDB files.  It is available in two forms, as Matlab code that has been tested on the PC, Macintosh, and UNIX, and as a PC executable version that does not require a Matlab license.  Releases, features, and known bugs are listed chronologically at the bottom of this page. 

Screen shot of the FR3D graphical user interface.  The query motif comes from the PDB file 1s72.  It consists of nucleotides 2701, 2702, 2703, 2691, 2693, and 2694.  The search to be conducted is a mixed geometric and symbolic search.  Candidate motifs must have the three indicated basepairs.

Paper to cite:  FR3D: Finding Local and Composite Recurrent Structural Motifs in RNA 3D Structures, Michael Sarver; Craig L. Zirbel; Jesse Stombaugh; Ali Mokdad; Neocles B. Leontis. Journal of Mathematical Biology (2008) 56:215–252.  Article in pdf format

User's manual: (3 MB)  Describes how to install the Matlab code and the PC executable version, how to start FR3D, and how to conduct searches.  In order to run the PC executable version, you will need the Matlab MCR installer (150 MB).

Documentation:  Describes each Matlab program in FR3D and displays the dependency between them.  Matlab users can run additional programs to analyze basepairs.

Additional PDB files are available at the RCSB Protein Data Bank

Requests for information and bug reports should be sent to Craig L. Zirbel at .

Downloads and release history

By downloading the software, you implicitly agree to the terms of use.

June 11, 2012 - Matlab code (8.4 MB, Matlab code, PDB files)

Various stability updates.

April 3, 2009 - Starter package (9 MB, Matlab code, PC executable, PDB files)

When displaying candidates, one can order them by centrality or by geometric similarity.  One can navigate through the candidates using a graphical display of the discrepancies between candidates.  FR3D now classifies base-phosphate interactions, and one can specify base-phosphate interactions in searches.  One can also specify whether an interaction should be nested or long-range.  The user's manual, however, is out of date.

May 16, 2008 - Starter package (8 MB, Matlab code, PC executable, PDB files) - Matlab code (548 KB)

Basepairing categories have been updated.  Many bugs have been fixed.  The Starter package contains the right file and directory structure, plus the Matlab source code and PC executable.  Visit to download analyzed files from many PDB files.  They should be stored in FR3D/PrecomputedData.

August 17, 2007 - Starter package (20 MB, Matlab code, PC executable, PDB files) - Matlab code (548 KB) - PC Executable (684 KB)

Base-phosphate interactions have been added; they are coded BP or PB in the search boxes. The previous alignment bug has been fixed. A bug in the August 16, 2007 version has been fixed.

March 19, 2007 - Starter package (29 MB, Matlab code, PC executable, PDB files) - Matlab code (747KB) - PC Executable (605KB)

The starter package makes it easier for first-time users to download FR3D and start using it.  A new option has been added to the Display Candidates menu, the ability to make scatterplots of the parameters describing pairs of nucleotides in the candidates.  Known bugs:  the alignment of candidates is sometimes incorrect; figure windows sometimes have incorrect names.

January 26, 2007 - Matlab code (514KB) - 4 analyzed PDB files (24MB)

Substantial changes have been made.  The basepairing criteria have been updated.  FR3D now stores small versions of analyzed files to reduce memory usage and decrease startup time.  The user can create lists of PDB files to more easily manage searches.  Many additional symbolic constraints are allowed.  The listing of candidates makes it easier to spot local and composite motifs, and to identify conserved features between candidates.  Additional display features allow sorting candidates by centrality, grouping them into clusters, and showing an alignment of the nucleotides in the candidates.  There is now a User's manual and other documentation.

August 29, 2006 - Matlab code (550KB) - 4 analyzed PDB files (17MB)

A PC executable version is now provided; see links above.  Users may make and maintain lists of PDB files to search.  To do so, make a text file called MyList_list.pdb with the name (no extension) of each PDB file on a separate line, then save it in the folder PDBFiles.  Bugs noted in the previous release have been fixed. Bugs: 1. With the PC executable, you cannot copy the list of candidates found from the console window.  2. With the PC executable, you cannot "View Query" by checking the checkbox on the GUI.

July 25, 2006 - Matlab code - link to 1s72 PDB file

A graphical user interface (GUI), written by Ali Mokdad, has been added.  The program is more stable.  Facilities have been added to mark candidates, to group them, to sort them by centrality to find a centroid, to produce a motif alignment, and to write them to a PDB file.  NMR files are handled by spacing each version of the structure by 1000 Angstroms to prevent "interactions" between different copies of the same structure.  Bugs:  1. The query motif must be from the first chain in the file.  2. Only query motifs of 9 nucleotides or smaller can be used.

April 6, 2006 - Matlab code and one PDB file

Run the program FR3D and follow the directions in its header line.

Last modified 2012-06-11 /