RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures

Area of Science:

• Structural Biology
• Biochemistry
• Computational Biology

Background:

• Flexible fitting is crucial for modeling molecular structures into cryo-EM maps.
• Identifying rigid bodies optimizes model-map fit, particularly for large conformational changes.
• Existing tools for rigid body identification are limited to protein structures, lacking support for nucleic acids.

Purpose of the Study:

• To extend the RIBFIND program for identifying rigid bodies in nucleic acid structures.
• To develop a tool for analyzing RNA dynamics and improving cryo-EM model refinement.
• To address the growing need for computational tools in RNA structural biology.

Main Methods:

• Extension of the RIBFIND algorithm to handle nucleic acid structures.
• Application of RIBFIND2 to identify rigid bodies in complex RNA structures.
• Demonstration of RIBFIND2's utility in cryo-EM model refinement using a hierarchical approach.

Main Results:

• RIBFIND2 successfully identifies biologically relevant rigid bodies in complex RNA structures.
• The tool captures a wide range of RNA dynamics, including significant rigid-body movements.
• Hierarchical refinement using RIBFIND2-assigned rigid bodies showed advantages over classical all-atom refinement in cryo-EM model building.

Conclusions:

• RIBFIND2 provides a valuable tool for analyzing RNA structures and dynamics.
• The identified rigid bodies enhance the accuracy and efficiency of cryo-EM model refinement for RNA.
• RIBFIND2 is accessible as a web server and a standalone tool, supporting structural biology research.