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.
- Windows / Mac / Linux
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RNABC 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)
RNABC is free software available under the terms of its own BSD-style license.