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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

CyloFold: secondary structure prediction including pseudoknots.

Eckart Bindewald¹, Tanner Kluth, Bruce A Shapiro

¹Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA.

Nucleic Acids Research

|May 27, 2010

Summary

This study introduces a novel computational method for RNA secondary structure prediction that handles complex pseudoknots. The approach simulates RNA folding and checks for steric feasibility, offering a competitive alternative to existing tools.

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Area of Science:

Computational biology
Molecular modeling
Bioinformatics

Background:

RNA secondary structure prediction is crucial for understanding RNA function.
Existing methods often limit pseudoknot complexity due to computational constraints.
Handling complex pseudoknots remains a significant challenge in the field.

Purpose of the Study:

To develop a computational method for RNA secondary structure prediction without restrictions on pseudoknot complexity.
To incorporate a steric feasibility check within the folding simulation.
To evaluate the performance of the new method against established RNA structure prediction tools.

Main Methods:

Simulating RNA folding in a coarse-grained manner.
Selecting helices based on established energy rules.
Utilizing a coarse-grained 3D model to assess steric feasibility during folding.

Main Results:

The developed method demonstrates competitive performance on datasets of 26 and 241 RNA sequences.
It successfully predicts RNA secondary structures with complex pseudoknots.
The approach shows comparable accuracy to pknotsRG, HotKnots, and UnaFold.

Conclusions:

The new method overcomes algorithmic limitations in pseudoknot prediction.
It provides a robust tool for RNA secondary structure prediction with complex pseudoknots.
The integration of steric feasibility testing enhances prediction accuracy and reliability.