Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24923
Abstract: Recasting temperature replica exchange (T‐RE) as a special case of Gibbs sampling has led to a simple and efficient scheme for enhanced mixing (Chodera and Shirts, J. Chem. Phys., 2011, 135, 194110). To critically examine… read more here.
Keywords: independence sampling; replica exchange; simulations ordered; ordered disordered ... See more keywords
Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26887
Abstract: Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional… read more here.
Keywords: replica exchange; replica; simulation studies; amide bond ... See more keywords
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of computational chemistry"
DOI: 10.1002/jcc.27124
Abstract: Generalized replica exchange with solute tempering (gREST) is one of the enhanced sampling algorithms for proteins or other systems with rugged energy landscapes. Unlike the replica-exchange molecular dynamics (REMD) method, solvent temperatures are the same… read more here.
Keywords: replica exchange; generalized replica; exchange solute; exchange ... See more keywords
Optimization of replica exchange temperature ladder under the well-tempered ensemble
Sign Up to like & getrecommendations! Published in 2018 at "Chemical Physics Letters"
DOI: 10.1016/j.cplett.2018.09.036
Abstract: Abstract Selection of temperature sequence and bias factor is a critical step for the preparation of Parallel Tempering simulations in a Well-Tempered Ensemble (PT-WTE). We provide a scheme in this study to generate the temperature… read more here.
Keywords: temperature; optimization replica; well tempered; replica exchange ... See more keywords
A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints.
Sign Up to like & getrecommendations! Published in 2019 at "Methods"
DOI: 10.1016/j.ymeth.2019.05.001
Abstract: We present a 2D replica exchange protocol incorporating secondary structure information to dramatically improve 3D RNA folding using molecular dynamics simulations. We show that incorporating base-pairing restraints into all-atom, explicit solvent simulations enables the accurate… read more here.
Keywords: molecular dynamics; replica exchange; rna; rna folding ... See more keywords
Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00065
Abstract: RNA is a key participant in many biological processes, but studies of RNA using computer simulations lag behind those of proteins, largely due to less-developed force fields and the slow dynamics of RNA. Generating converged… read more here.
Keywords: replica exchange; structure; rna; ensemble convergence ... See more keywords
Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c01139
Abstract: Replica exchange with solute tempering (REST) is a highly effective variant of replica exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling the Hamiltonian for a selected "solute" region of the system,… read more here.
Keywords: replica exchange; exchange solute; exchange; solute solvent ... See more keywords
Alchemical Free Energy and Hamiltonian Replica Exchange Molecular Dynamics to Compute Hydrofluorocarbon Isotherms in Imidazolium-Based Ionic Liquids.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.3c00206
Abstract: Ionic liquids (ILs) have shown promise for applications that leverage differential gas solubility in an IL solvent, e.g., gas separations. Although most available literature provides Henry's law constants, the ability to efficiently estimate full isotherms… read more here.
Keywords: replica exchange; solubility; energy; hamiltonian replica ... See more keywords
Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract
Sign Up to like & getrecommendations! Published in 2021 at "Scientific Reports"
DOI: 10.1038/s41598-021-02728-8
Abstract: Crystallins are ubiquitous, however, prevalence is seen in eye lens. Eye lens crystallins are long-lived and structural intactness is required for maintaining lens transparency and protein solubility. Mutations in crystallins often lead to cataract. In… read more here.
Keywords: replica exchange; eye lens; exchange molecular; sites crystallin ... See more keywords
Replica exchange molecular dynamics study of the amyloid beta (11–40) trimer penetrating a membrane
Sign Up to like & getrecommendations! Published in 2017 at "RSC Advances"
DOI: 10.1039/c6ra26461a
Abstract: Alzheimer's disease is characterized by the interaction of neurotoxic Aβ oligomers with cellular membranes, which disturbs ion homeostasis. To determine the putative structures of the transmembrane 3Aβ11–40 oligomer, temperature replica exchange molecular dynamics (REMD) simulations… read more here.
Keywords: molecular dynamics; replica exchange; structure; membrane ... See more keywords
Temperature-mediated switching of protectant-denaturant behavior of trimethylamine-N-oxide and consequences on protein stability from a replica exchange molecular dynamics simulation study
Sign Up to like & getrecommendations! Published in 2017 at "Molecular Simulation"
DOI: 10.1080/08927022.2016.1233546
Abstract: Abstract The detailed mechanism of protein folding–unfolding processes with the aid of osmolytes has been a leading topic of discussion over many decades. We have used replica-exchange molecular dynamics simulation to propose the molecular mechanism… read more here.
Keywords: temperature; molecular dynamics; replica exchange; simulation ... See more keywords