Vfold-Pipeline

Vfold-Pipeline predicts RNA secondary and tertiary (3D) structures from nucleotide sequences to provide computational 3D conformations for studies of RNA structure and function.

Key Features:

• Integrated components: Integration of three core programs—Vfold2D, Vfold3D, and VfoldLA—each contributing to the structure prediction process.
• Vfold2D: Capable of incorporating SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension) experimental data to constrain and improve RNA secondary-structure predictions.
• Vfold3D: Uses a 3D template database to generate RNA tertiary-structure predictions or initial 3D models.
• VfoldLA: Participates in the integrated prediction workflow to support structure modeling alongside Vfold2D and Vfold3D.
• Rfam constraints: Automatic extraction of 2D structural constraints from the Rfam database to inform secondary-structure prediction.
• Expanded 3D template database: Inclusion of various RNA motifs in the 3D template library to improve generation of accurate 3D structures or initial models suitable for further refinement or validation.

Scientific Applications:

• RNA structural modeling: Generation of secondary and tertiary RNA structures for studies of RNA structure and function.
• Functional and interaction analysis: Provision of 3D models to support investigation of RNA interactions and functional hypotheses.
• Experimental planning and validation: Production of predicted or initial models to guide experimental design and downstream validation.
• Drug discovery: Support for RNA-targeted drug design and therapeutic development through provision of structural models.

Methodology:

Integration of Vfold2D, Vfold3D, and VfoldLA; Vfold2D incorporation of SHAPE experimental data; automatic extraction of 2D constraints from Rfam; and use of an expanded 3D template database to generate 3D predictions or initial structures.