Biomolecules under mechanical force

S Kumar, MS Li - Physics Reports, 2010 - Elsevier
Recent advances in single molecule experiments have raised many challenges. These
challenges can be met by a proper understanding of the inter-and intra-molecular …

Cluster variation method in statistical physics and probabilistic graphical models

A Pelizzola - Journal of Physics A: Mathematical and General, 2005 - iopscience.iop.org
The cluster variation method (CVM) is a hierarchy of approximate variational techniques for
discrete (Ising-like) models in equilibrium statistical mechanics, improving on the mean-field …

Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models

K Ooka, M Arai - Nature Communications, 2023 - nature.com
Recent breakthroughs in highly accurate protein structure prediction using deep neural
networks have made considerable progress in solving the structure prediction component of …

Coordinate-dependent diffusion in protein folding

RB Best, G Hummer - … of the National Academy of Sciences, 2010 - National Acad Sciences
Diffusion on a low-dimensional free-energy surface is a remarkably successful model for the
folding dynamics of small single-domain proteins. Complicating the interpretation of both …

Measuring internal friction of an ultrafast-folding protein

T Cellmer, ER Henry, J Hofrichter… - Proceedings of the …, 2008 - National Acad Sciences
Nanosecond laser T-jump was used to measure the viscosity dependence of the folding
kinetics of the villin subdomain under conditions where the viscogen has no effect on its …

Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations

ER Henry, RB Best, WA Eaton - Proceedings of the …, 2013 - National Acad Sciences
Advances in computing have enabled microsecond all-atom molecular dynamics trajectories
of protein folding that can be used to compare with and test critical assumptions of …

Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone

I Roterman, K Stapor, L Konieczny - BMC bioinformatics, 2023 - Springer
Background The aqueous environment directs the protein folding process towards the
generation of micelle-type structures, which results in the exposure of hydrophilic residues …

Combinatorial modeling of protein folding kinetics: free energy profiles and rates

ER Henry, WA Eaton - Chemical Physics, 2004 - Elsevier
A combinatorial approach has been used to determine the optimal assumptions and
robustness of simple statistical mechanical models for protein folding. By combining …

On the role of native contact cooperativity in protein folding

D Wang, LB Frechette, RB Best - Proceedings of the …, 2024 - National Acad Sciences
The consistency of energy landscape theory predictions with available experimental data, as
well as direct evidence from molecular simulations, have shown that protein folding …

Predictions from an Ising-like statistical mechanical model on the dynamic and thermodynamic effects of protein surface electrostatics

AN Naganathan - Journal of chemical theory and computation, 2012 - ACS Publications
Charged residues on the surface of a protein are known hot-spots for post-translational
modification, protein/ligand-binding, and tuning conformational stabilities. Recent …