Journal of Mathematical Biology

, Volume 56, Issue 1, pp 253–278

RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone

  • Xueyi Wang
  • Gary Kapral
  • Laura Murray
  • David Richardson
  • Jane Richardson
  • Jack Snoeyink
Article

DOI: 10.1007/s00285-007-0082-x

Cite this article as:
Wang, X., Kapral, G., Murray, L. et al. J. Math. Biol. (2008) 56: 253. doi:10.1007/s00285-007-0082-x

Abstract

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 

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Xueyi Wang
    • 1
  • Gary Kapral
    • 2
  • Laura Murray
    • 2
  • David Richardson
    • 2
  • Jane Richardson
    • 2
  • Jack Snoeyink
    • 1
  1. 1.Department of Computer ScienceUNC Chapel HillChapel HillUSA
  2. 2.Department of BiochemistryDuke UniversityDurhamUSA

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