The Protein-Folding Abort Problem

Abstract

This working paper introduces the Protein-Folding Abort Problem as a finite-horizon, set-valued decision framework for determining whether a protein conformation still retains an admissible route to a declared functional folding target. Rather than equating misfolding, kinetic trapping, or low structural similarity with irreversible failure, the framework classifies states as robustly recoverable, conditionally recoverable, abort, or unresolved under bounded model and environmental uncertainty. The approach extends committor-based reasoning by incorporating explicit system boundaries, finite observation horizons, rescue mechanisms, uncertainty sets, abort boundaries, and first loss-of-recoverability times. It includes preregistered validation and falsification criteria for fast-folding systems, topological traps, and assisted rescue. The framework is theoretical and non-operational and does not claim a universal microscopic solution to protein folding.