Physics-based computational and theoretical approaches to intrinsically disordered proteins
Highlights•Liquid-liquid phase separation underlies the formation of membraneless
organelles within cells.•Theory and molecular simulations help to relate interactions at the …
organelles within cells.•Theory and molecular simulations help to relate interactions at the …
Challenges in protein-folding simulations
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 …
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 …
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 …
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 …
optionally velocities and energies) as a function of time and provide a representation of the …
A bias-exchange approach to protein folding
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 …
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
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 …
features with larger globular proteins. Although the system has been intensively investigated …
Equilibrium study of protein denaturation by urea
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 …
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
Auto-associative neural networks (“autoencoders”) present a powerful nonlinear
dimensionality reduction technique to mine data-driven collective variables from molecular …
dimensionality reduction technique to mine data-driven collective variables from molecular …
Accelerated molecular dynamics simulations of protein folding
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 …
domain, was simulated via accelerated molecular dynamics (aMD). In comparison with …