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RNABC

RNABC (RNA Backbone Correction) is designed for reducing the steric clashes in dinucleotides of existing RNA backbone structures. It first fixes the phosphate and base positions, which are the clearest parts in X-ray crystallography structure, and then reconstructs the remaining atoms of the dinucleotide using forward kinematics and conjugate gradient method. The input parameters, like bond lengths, bond angles, and sugar pucker types, are from canonical values or specified by users. The output results cluster the possible suite conformations (from base to base) without steric clashes.

The animation at left shows a RNABC assisted fix of a clash in chain 0 of 1JJ2 (hydrogens added with Reduce, contact dots kinemage generated by Probe). In the "before" image note the pink spikes between residues 870 & 871 indicating an improbable overlap of van der Waals shells. The "after" image shows the positions suggested by RNABC showing excellent contacts.

RNABC is created by Xueyi Wang and Prof. Jack Snoeyink at Department of Computer Science, University of North Carolina at Chapel Hill, with the collaboration of the Richardson Lab. The program is described in X. Wang, G. Kapral, L. Murray, D. Richardson, J. Richardson & J. Snoeyink. "RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone". Journal Mathematical Biology (published January 2008, doi: 10.1007/s00285-007-0082)

If you have any questions or suggestions for RNABC, please email to xwang@nnu.edu.

To download: click the program file name for the appropriate table-row. Program use instructions are included in the download bundles.


Platform Version Release date Download size Program
(click to download)
Linux 1.11 19-May-09 293 (Kb) download arrow rnabc.1.11.090519.linuxi386.zip
Windows 1.11 19-May-09 437 (Kb) download arrow rnabc.1.11.090519.win.zip
Mac OS X 1.11 19-May-09 298 (Kb) download arrow rnabc.1.11.090519.mac.zip
Source code 1.11 19-May-09 402 (Kb) download arrow rnabc.1.11.090519.src.zip