Physics-based computational and theoretical approaches to intrinsically disordered proteins

JE Shea, RB Best, J Mittal - Current opinion in structural biology, 2021 - Elsevier
Highlights•Liquid-liquid phase separation underlies the formation of membraneless
organelles within cells.•Theory and molecular simulations help to relate interactions at the …

Challenges in protein-folding simulations

PL Freddolino, CB Harrison, Y Liu, K Schulten - Nature physics, 2010 - nature.com
Experimental studies of protein folding are hampered by the fact that only low-resolution
structural data can be obtained with sufficient temporal resolution. Molecular dynamics …

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

A Laio, FL Gervasio - Reports on Progress in Physics, 2008 - iopscience.iop.org
Metadynamics is a powerful algorithm that can be used both for reconstructing the free
energy and for accelerating rare events in systems described by complex Hamiltonians, at …

Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration

W Chen, AL Ferguson - Journal of computational chemistry, 2018 - Wiley Online Library
Macromolecular and biomolecular folding landscapes typically contain high free energy
barriers that impede efficient sampling of configurational space by standard molecular …

Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms

J Shao, SW Tanner, N Thompson… - Journal of chemical …, 2007 - ACS Publications
Molecular dynamics simulation methods produce trajectories of atomic positions (and
optionally velocities and energies) as a function of time and provide a representation of the …

A bias-exchange approach to protein folding

S Piana, A Laio - The journal of physical chemistry B, 2007 - ACS Publications
By suitably extending a recent approach [Bussi, G.; et al. J. Am. Chem. Soc. 2006, 128,
13435] we introduce a powerful methodology that allows the parallel reconstruction of the …

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations

F Marinelli, F Pietrucci, A Laio… - PLoS computational …, 2009 - journals.plos.org
Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several
features with larger globular proteins. Although the system has been intensively investigated …

Equilibrium study of protein denaturation by urea

DR Canchi, D Paschek, AE García - Journal of the American …, 2010 - ACS Publications
Though urea is commonly used to denature proteins, the molecular mechanism of its
denaturing ability is still a subject of considerable debate. Previous molecular dynamics …

[HTML][HTML] Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design

W Chen, AR Tan, AL Ferguson - The Journal of chemical physics, 2018 - pubs.aip.org
Auto-associative neural networks (“autoencoders”) present a powerful nonlinear
dimensionality reduction technique to mine data-driven collective variables from molecular …

Accelerated molecular dynamics simulations of protein folding

Y Miao, F Feixas, C Eun… - Journal of computational …, 2015 - Wiley Online Library
Folding of four fast‐folding proteins, including chignolin, Trp‐cage, villin headpiece and WW
domain, was simulated via accelerated molecular dynamics (aMD). In comparison with …