Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation
is difficult to determine, and most existing RNA structures show serious steric clashes (≥ 0.4 Å overlap) when hydrogen atoms
are taken into account. We have developed a program called RNABC (RNA Backbone Correction) that performs local perturbations
to search for alternative conformations that avoid those steric clashes or other local geometry problems. Its input is an
all-atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with problem areas specified.
RNABC rebuilds a suite (the unit from sugar to sugar) by anchoring the phosphorus and base positions, which are clearest in
crystallographic electron density, and reconstructing the other atoms using forward kinematics. Geometric parameters are constrained
within user-specified tolerance of canonical or original values, and torsion angles are constrained to ranges defined through
empirical database analyses. Several optimizations reduce the time required to search the many possible conformations. The
output results are clustered and presented to the user, who can choose whether to accept one of the alternative conformations.
Two test evaluations show the effectiveness of RNABC, first on the S-motifs from 42 RNA structures, and second on the worst
problem suites (clusters of bad clashes, or serious sugar pucker outliers) in 25 unrelated RNA structures. Among the 101 S-motifs,
88 had diagnosed problems, and RNABC produced clash-free conformations with acceptable geometry for 71 of those (about 80%).
For the 154 worst problem suites, RNABC proposed alternative conformations for 72. All but 8 of those were judged acceptable
after examining electron density (where available) and local conformation. Thus, even for these worst cases, nearly half the
time RNABC suggested corrections suitable to initiate further crystallographic refinement. The program is available from
http://kinemage.biochem.duke.edu.
Keywords Kinematic chain - RNA backbone conformation - RNA backbone adjustment - RNA crystallography - Automated rebuilding - Steric clash - S-motifs - All-atom contacts - Structure validation
Mathematics Subject Classification (2000) 92E10 - 92-04