SEPAS

SEPAS predicts protein dimer stability by estimating mechanical properties of binding interfaces from 3D structural data to classify dimers into stability/affinity classes.

Key Features:

• Mechanical Stiffness Prediction: Predicts the mechanical stiffness of the protein binding patch (PBP) region on a single subunit and links stiffness to experimentally measured affinities.
• Classwise Stability Prediction: Classifies protein dimers into distinct stability/affinity classes based on computed mechanical properties, with a reported minimum accuracy of 0.72.
• Interface-Specific Analysis: Constructs interface-specific recurrence plots and applies recurrence quantitative analysis (RQA) to assess topological properties and amino acid affinities at protein interaction interfaces.
• Comparative Mechanical Properties: Compares mechanical properties of binding patches with nonbinding regions, observing that stable dimers typically have mechanically softer interfaces than unstable ones.
• Structural Inputs and Metrics: Operates on 3D structural data of protein subunits and utilizes metrics such as accessible surface area (ASA) and distance matrices.

Scientific Applications:

• Deciphering Protein Complex Behavior: Linking interface mechanical properties to dimer stability to inform on the stability and function of protein complexes.
• Therapeutic Manipulation: Identifying interface characteristics that can be targeted to modulate protein–protein interactions.
• Structural Analysis: Providing a mechanical-property–centered approach to analyzing protein interfaces in structural biology studies.

Methodology:

Analyzes 3D structures to predict mechanical stiffness of the PBP, constructs interface-specific recurrence plots, applies recurrence quantitative analysis (RQA), computes accessible surface area (ASA) and distance matrices, and classifies dimers into stability classes.