ValFold

ValFold predicts secondary structures of DNA and RNA aptamers, capturing canonical Watson-Crick base pairs and G-G pairs derived from G-quadruplex formations to support aptamer design and optimization.

Key Features:

• Enhanced Prediction Accuracy: Predicts both canonical Watson-Crick base pairs and G-G pairs derived from G-quadruplex structures to improve secondary structure accuracy.
• Stem Candidate Selection Algorithm: Uses a stem candidate selection algorithm that identifies and evaluates potential stem regions within nucleic acid sequences.
• Aptamer-Specific Design: Tailors predictions to aptamers selected via Systematic Evolution of Ligands by EXponential enrichment (SELEX) and accounts for aptamer-specific properties without altering binding affinity.

Scientific Applications:

• Optimize Aptamer Design: Facilitates truncation or minimization of sequences while maintaining functional integrity.
• Introduce Chemical Modifications: Enables targeted chemical modifications without affecting binding affinity.
• Advance SELEX Processes: Provides structural insights to support selection of high-affinity aptamers in SELEX workflows.

Methodology:

ValFold applies a stem candidate selection algorithm that identifies and evaluates potential stem regions and recognizes canonical Watson-Crick base pairs and G-G pairs from G-quadruplex formations to predict secondary structures.