ProtEvol

ProtEvol generates independent site-specific amino acid distributions using a mean-field substitution model that incorporates stability constraints.

Key Features:

• Mean-Field Substitution Model: Generates amino acid distributions constrained by protein stability.
• Background Distribution and Selection Parameter: Optimizes background distribution and a selection parameter to produce realistic protein sequence likelihoods.

Scientific Applications:

• Molecular Biology and Bioinformatics: Simulates protein evolution while maintaining structural integrity to support evolutionary studies.

Methodology:

Develops a mean-field substitution model with stability constraints, uses analytic solutions to characterize site-specific distributions, and refines models through empirical data comparison.