Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
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Path Similarity Analysis: A Method for Quantifying Macromolecular PathwaysEnhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolinEvaluation of solvation free energies for small molecules with the AMOEBA polarizable force fieldDevelopment of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data.Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments.Extended molecular dynamics of a c-kit promoter quadruplex.Antibodyomics: bioinformatics technologies for understanding B-cell immunity to HIV-1.Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations.Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A ReviewAll-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.Polymorphism at 129 dictates metastable conformations of the human prion protein N-terminal β-sheet.Atomistic-level portrayal of drug-DNA Interplay: a history of courtships and meetings revealed by molecular simulations.Theoretical and computational studies of peptides and receptors of the insulin family.Protein Flexibility in Drug Discovery: From Theory to Computation.Methods of probing the interactions between small molecules and disordered proteins.Exploiting computationally derived out-of-the-box protein conformations for drug design.How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes.Comparison of force fields for Alzheimer's A β42: A case study for intrinsically disordered proteins.Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents.ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.Evaluation of Ochratoxin Recognition by Peptides Using Explicit Solvent Molecular DynamicsBeyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistryIntrinsic map dynamics exploration for uncharted effective free-energy landscapes.Dynamic free energy surfaces for sodium diffusion in type II silicon clathrates.Dynamic Docking: A Paradigm Shift in Computational Drug Discovery.CO2 packing polymorphism under pressure: Mechanism and thermodynamics of the I-III polymorphic transition.Flap Dynamics in Aspartic Proteases: A Computational Perspective.Efficient free energy calculations by combining two complementary tempering sampling methods.Energetics and structural characterization of the "DFG-flip" conformational transition of B-RAF kinase: a SITS molecular dynamics study.Adaptive-numerical-bias metadynamics.Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling.Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics.Communication: Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering.Properties of low-dimensional collective variables in the molecular dynamics of biopolymers.Effective dynamics along given reaction coordinates, and reaction rate theory.Replica state exchange metadynamics for improving the convergence of free energy estimates.Role of Conformational Motions in Enzyme Function: Selected Methodologies and Case Studies.
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
description
article
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im Dezember 2013 veröffentlichter wissenschaftlicher Artikel
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wetenschappelijk artikel
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наукова стаття, опублікована в грудні 2013
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name
Enhanced Sampling in Molecular ...... , and Temperature-Acceleration
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Enhanced Sampling in Molecular ...... , and Temperature-Acceleration
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type
label
Enhanced Sampling in Molecular ...... , and Temperature-Acceleration
@en
Enhanced Sampling in Molecular ...... , and Temperature-Acceleration
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prefLabel
Enhanced Sampling in Molecular ...... , and Temperature-Acceleration
@en
Enhanced Sampling in Molecular ...... , and Temperature-Acceleration
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P2860
P356
P1433
P1476
Enhanced Sampling in Molecular ...... , and Temperature-Acceleration
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P2093
Cameron Abrams
Giovanni Bussi
P2860
P304
P356
10.3390/E16010163
P577
2013-12-27T00:00:00Z