PredyFlexy

PredyFlexy predicts local protein structures and estimates residue-level flexibility from amino acid sequences to characterize protein dynamics.

Key Features:

• Structural alphabet / LSP library: Uses a structural alphabet based on a library of Structural Prototypes (LSPs) to represent recurring local protein structures.
• Prediction methodology: Predicts structural candidates as LSP assignments and estimates average flexibility along the sequence from the predicted local structures without using sophisticated learning algorithms.
• Flexibility descriptors: Quantifies flexibility using X-ray B-factors and root mean square fluctuations (RMSF) calculated from molecular dynamics simulations.
• Flexibility classes: Classifies protein regions into three predefined flexibility classes based on combined analysis of B-factors and RMSF.

Scientific Applications:

• Enzyme mechanism analysis: Interprets residue-level dynamics relevant to catalytic function and active-site mobility.
• Drug design and discovery: Identifies flexible and rigid regions that inform ligand binding and target selection.
• Protein–protein interaction studies: Maps dynamic regions that may mediate interaction interfaces.
• Disease-related conformational change investigation: Investigates conformational changes associated with disease states by highlighting altered flexibility patterns.

Methodology:

Assigns local structural motifs using the LSP library and estimates residue-level flexibility by integrating predicted local structures with X-ray B-factors and RMSF from molecular dynamics simulations to classify residues into three predefined flexibility classes.