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

Area of Science:

• Structural Biology
• Computational Biology
• Biochemistry

Background:

• Accurate RNA structure is crucial for understanding RNA function.
• Existing RNA structures often exhibit steric clashes when hydrogen atoms are included.
• Determining precise RNA backbone conformation remains challenging.

Purpose of the Study:

• To develop a computational tool for correcting steric clashes and geometric problems in RNA structures.
• To improve the accuracy of all-atom RNA models derived from crystallographic data.

Main Methods:

• Developed RNABC (RNA Backbone Correction) software for local backbone perturbations.
• Input: All-atom RNA crystal structure coordinates; Output: Alternative, clash-free conformations.
• Anchored phosphorus and base positions; reconstructed other atoms using forward kinematics with constrained geometry.

Main Results:

• RNABC resolved clash-free conformations for 71% of problematic S-motifs (80% success rate).
• For severe problem suites, RNABC proposed acceptable alternative conformations in nearly 50% of cases.
• Suggested corrections were suitable for initiating further crystallographic refinement.

Conclusions:

• RNABC effectively identifies and corrects steric clashes and geometric issues in RNA structures.
• The program enhances the accuracy of RNA structural models, aiding functional studies.
• RNABC provides a valuable tool for refining RNA crystal structures.