Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25520
Abstract: Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation. Biased sampling can artificially drive the simulation along prespecified collective variables (CVs),… read more here.
Keywords: enhanced sampling; molecular enhanced; energy; exploration ... See more keywords
CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods
Sign Up to like & getrecommendations! Published in 2022 at "Protein Science"
DOI: 10.1002/pro.4446
Abstract: Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM‐GUI… read more here.
Keywords: gui enhanced; enhanced sampling; enhanced sampler; charmm gui ... See more keywords
An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.1c01024
Abstract: We introduce a novel multilevel enhanced sampling strategy grounded on Gaussian-accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We introduce the new "dual-water" mode and its… read more here.
Keywords: enhanced sampling; multilevel enhanced; polarizable force; force ... See more keywords
Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.1c01222
Abstract: Atomistic molecular dynamics simulations represent an established technique for investigation of RNA structural dynamics. Despite continuous development, contemporary RNA simulations still suffer from suboptimal accuracy of empirical potentials (force fields, ffs) and sampling limitations. Development… read more here.
Keywords: enhanced sampling; rna tetraloops; toward convergence; convergence ... See more keywords
LINES: Log-Probability Estimation via Invertible Neural Networks for Enhanced Sampling.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00254
Abstract: It is very challenging to sample a molecular process with large activation energies using molecular dynamics simulations. Current enhanced sampling methodologies, such as umbrella sampling and metadynamics, rely on the identification of appropriate reaction coordinates… read more here.
Keywords: enhanced sampling; probability estimation; reaction; log probability ... See more keywords
MDexciteR: Enhanced Sampling Molecular Dynamics by Excited Normal Modes or Principal Components Obtained from Experiments.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00599
Abstract: Molecular dynamics with excited normal modes (MDeNM) is an enhanced sampling method for exploring conformational changes in proteins with minimal biases. The excitation corresponds to injecting kinetic energy along normal modes describing intrinsic collective motions.… read more here.
Keywords: enhanced sampling; molecular dynamics; normal modes; excited normal ... See more keywords
Rare Event Kinetics from Adaptive Bias Enhanced Sampling.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00806
Abstract: We introduce a novel enhanced sampling approach named on-the-fly probability enhanced sampling (OPES) flooding for calculating the kinetics of rare events from atomistic molecular dynamics simulation. This method is derived from the OPES approach [Invernizzi… read more here.
Keywords: enhanced sampling; adaptive bias; rare event; kinetics adaptive ... See more keywords
Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00873
Abstract: Enhanced sampling methods are indispensable in computational chemistry and physics, where atomistic simulations cannot exhaustively sample the high-dimensional configuration space of dynamical systems due to the sampling problem. A class of such enhanced sampling methods… read more here.
Keywords: learning collective; enhanced sampling; reweighted manifold; manifold learning ... See more keywords
Studying Disease-Associated UBE3A Missense Variants Using Enhanced Sampling Molecular Simulations
Sign Up to like & getrecommendations! Published in 2022 at "ACS Omega"
DOI: 10.1021/acsomega.2c00959
Abstract: Missense variants in UBE3A underlie neurodevelopmental conditions such as Angelman Syndrome and Autism Spectrum Disorder, but the underlying molecular pathological consequences on protein folding and function are poorly understood. Here, we report a novel, maternally… read more here.
Keywords: sampling molecular; enhanced sampling; missense; missense variants ... See more keywords
Enhanced Sampling Aided Design of Molecular Photoswitches.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.2c04419
Abstract: Advances in the evolving field of atomistic simulations promise important insights for the design and fundamental understanding of novel molecular photoswitches. Here, we use state-of-the-art enhanced simulation techniques to unravel the complex, multistep chemistry of… read more here.
Keywords: sampling aided; design molecular; enhanced sampling; aided design ... See more keywords
Identification of 11β-HSD1 inhibitors through enhanced sampling methods.
Sign Up to like & getrecommendations! Published in 2022 at "Chemical communications"
DOI: 10.1039/d1cc06894f
Abstract: Aminoarylbenzosuberene (AAB) molecules were chosen for in silico analysis to develop effective and more competent 11β-hydroxysteroid dehydrogenase (11β-HSD1) protein inhibitors. The AAB4 molecule was shown to have stronger interactions and binding affinity than standard inhibitors… read more here.
Keywords: enhanced sampling; identification hsd1; hsd1; sampling methods ... See more keywords