Contact Q-value Analysis for Biomolecular Simulations
The q-value is the fraction of native residue–residue contacts retained when compared to a reference structure. The package includes some of the most common Q-value definitions:
Wolynes Q A smooth, distance-weighted score: every reference contact contributes via a Gaussian centered at its native distance, with width growing as a power of sequence separation.
Onuchic Q Similar Gaussian form as Wolynes, but only considers contacts beyond a minimum sequence gap and within a hard distance cutoff.
Interface Q Computes Wolynes-style Q only for pairs that lie in different chains or domains—ideal for monitoring binding or assembly.
Intrachain Q Restricts Wolynes Q to contacts within each chain separately—handy for multi-domain proteins or polymers.
Contact Q (Qc) A version of Wolynes Q where only interactions between residues in contact in the native structure are considered based on a distance cutoffs
Custom Q Other definitions can be implemented by providing a callable function.
Each method can be applied to Cα, Cβ, or any atom selection, with optional per-residue or per-contact outputs, and integrates with MDAnalysis.