Reply to Comment on "Criterion that Determines the Foldability of Proteins"

TL;DR

This paper clarifies that the correlation between folding times and the parameter sigma in protein-like models was known since 1993, and challenges the usefulness of energy gap as a predictor of folding times.

Contribution

It reaffirms the early established correlation between folding times and sigma, and refutes the significance of energy gap correlation in compact structures.

Findings

Correlation between folding times and sigma was established in 1993.

Folding times show no useful correlation with energy gap in compact structures.

The paper clarifies historical and theoretical misunderstandings in protein folding criteria.

Abstract

We point out that the correlation between folding times and $\sigma = (T_{\theta } - T_{f})/T_{\theta }$ in protein-like heteropolymer models where $T_{\theta }$ and $T_{f}$ are the collapse and folding transition temperatures was already established in 1993 before the other presumed equivalent criterion (folding times correlating with $T_{f}$ alone) was suggested. We argue that the folding times for these models show no useful correlation with the energy gap even if restricted to the ensemble of compact structures as suggested by Karplus and Shakhnovich (cond-mat/9606037).