Kim T. Simons

TL;DR: Investigations have revealed statistically significant correlations between the average sequence separation between contacting residues in the native state and the rate and transition state placement of folding for a non-homologous set of simple, single domain proteins, indicating that proteins featuring primarily sequence-local contacts tend to fold more rapidly and exhibit less compact folding transition states than those characterized by more non-local interactions.

TL;DR: The effects of multiple sequence information and different types of conformational constraints on the overall performance of the method are investigated, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures are investigated.

TL;DR: Results suggest that ab initio methods may soon become useful for low‐resolution structure prediction for proteins that lack a close homologue of known structure.

TL;DR: A scoring function based on the decomposition P(st structure|sequence) ∝ P(sequence|structure) *P(structure), which outperforms previous scoring functions in correctly identifying native‐like protein structures in large ensembles of compact decoys is described.

TL;DR: Recent experimental results suggest that despite a vast diversity of structures and functions, there are fundamental similarities in the folding mechanisms of single domain proteins and that a general and quantitative theory of protein folding rates and mechanisms may be near on the horizon.