FlexPred

FlexPred predicts residue positions that undergo ordered conformational switches in proteins by integrating sequence-derived information and structural data.

Key Features:

• Input Formats: Accepts protein sequences in FASTA format or structure files from the Protein Data Bank (PDB).
• Pattern Recognition Algorithm: Uses a pattern recognition algorithm trained on examples from the Database of Macromolecular Movements.
• Adjustable False Positive Rate: Allows adjustment of the false positive rate to balance sensitivity and specificity.
• Analytical Properties: Analyzes sequence neighbors, evolutionary conservation, solvent accessibility, and secondary structure patterns to detect conformational variability.
• Nonloop Region Detection: Identifies conformationally variable residue positions in helices, strands, buried regions, and solvent-accessible loops.

Scientific Applications:

• Understanding Protein Dynamics: Aids in elucidating structural changes proteins undergo during biological processes by predicting conformational switch residues.
• Functional Analysis: Provides insight into protein function and dysfunction by identifying less conserved, variable positions that may affect activity.
• Prion Protein Refolding: Has been applied to prion protein (PrP) to identify segments involved in refolding.

Methodology:

Applies a pattern recognition algorithm trained on the Database of Macromolecular Movements and integrates sequence-derived and structural inputs to evaluate sequence neighbors, evolutionary conservation, solvent accessibility, and secondary structure patterns.