4.7 Article

Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Physical

A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations

Paul A. Torrillo et al.

Summary: The minimal adaptive binning (MAB) scheme is a more efficient approach for generating transitions, pathway diversity, estimating rate constants, and sampling conformations compared to manual, fixed binning schemes. It is applicable to various rare-events sampling strategies that utilize progress coordinates.

JOURNAL OF PHYSICAL CHEMISTRY A (2021)

Review Chemistry, Multidisciplinary

Gaussian accelerated molecular dynamics: Principles and applications

Jinan Wang et al.

Summary: Gaussian accelerated molecular dynamics (GaMD) is a robust computational method that accelerates biomolecular simulations by adding a harmonic boost potential, allowing for energetic reweighting via cumulant expansion to accurately reconstruct free energy landscapes. Hybrid schemes with other enhanced sampling methods have been introduced to further improve sampling and free energy calculations, enabling efficient characterization of biomolecular dynamics and interactions.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2021)

Article Chemistry, Physical

The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations

Alex J. DeGrave et al.

Summary: The RED scheme is a new method for calculating rate constants more efficiently using the weighted ensemble path sampling strategy, which results in up to 50% greater efficiency in estimating rate constants. This scheme is able to correct for statistical bias and is applicable to various rare-event processes simulations, showing good performance in handling event duration distribution.

JOURNAL OF CHEMICAL PHYSICS (2021)

Article Chemistry, Physical

Overcoming Free-Energy Barriers with a Seamless Combination of a Biasing Force and a Collective Variable-Independent Boost Potential

Haochuan Chen et al.

Summary: GaWTM-eABF is a hybrid algorithm that introduces the GaMD softened potential into WTM-eABF, effectively overcoming free-energy barriers in orthogonal space and accurately recovering unbiased free-energy landscape. Numerical tests demonstrate that GaWTM-eABF reduces uncertainty in PMF calculation and converges faster than WTM-eABF.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Chemistry, Multidisciplinary

A glycan gate controls opening of the SARS-CoV-2 spike protein

Terra Sztain et al.

Summary: Through simulations, the study reveals the mechanism of spike protein receptor binding domain (RBD) opening in SARS-CoV-2 infection, highlighting the crucial role of N-glycan in facilitating RBD opening. This research represents a milestone in ensemble pathway simulations and provides a foundation for understanding the fundamental mechanisms of viral entry and infection.

NATURE CHEMISTRY (2021)

Article Chemistry, Physical

Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook

Sarwar Hussain et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Chemistry, Medicinal

Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach

Surl-Hee Ahn et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Physical

Scalable molecular dynamics on CPU and GPU architectures with NAMD

James C. Phillips et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Chemistry, Physical

Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian Microbin Analysis

Jeremy Copperman et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Multidisciplinary

Computational Estimation of Microsecond to Second Atomistic Folding Times

Upendra Adhikari et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Multidisciplinary Sciences

Atomic-level characterization of protein-protein association

Albert C. Pan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Chemistry, Physical

REVO: Resampling of ensembles by variation optimization

Nazanin Donyapour et al.

JOURNAL OF CHEMICAL PHYSICS (2019)

Article Chemistry, Physical

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors

Jinan Wang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2019)

Article Biochemistry & Molecular Biology

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations

Dalibor Trapl et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2019)

Article Chemistry, Physical

Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics

Yinglong Miao

JOURNAL OF CHEMICAL PHYSICS (2018)

Article Chemistry, Physical

Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation

Yu-ming M. Huang et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Chemistry, Multidisciplinary

Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions

Samuel D. Lotz et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Article Biochemistry & Molecular Biology

Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge

Tom Dixon et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2018)

Review Neurosciences

Molecular Dynamics Simulation for All

Scott A. Hollingsworth et al.

NEURON (2018)

Article Chemistry, Physical

Perspective: Identification of collective variables and metastable states of protein dynamics

Florian Sittel et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

Article Chemistry, Physical

Gaussian Accelerated Molecular Dynamics in NAMD

Yui Tik Pang et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)

Article Chemistry, Physical

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

Surl-Hee Ahn et al.

JOURNAL OF CHEMICAL PHYSICS (2017)

Article Chemistry, Physical

Kinetics from Replica Exchange Molecular Dynamics Simulations

Lukas S. Stelzl et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)

Article Biochemical Research Methods

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Peter Eastman et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Chemistry, Medicinal

Role of Molecular Dynamics and Related Methods in Drug Discovery

Marco De Vivo et al.

JOURNAL OF MEDICINAL CHEMISTRY (2016)

Article Engineering, Chemical

Engineering molecular dynamics simulation in chemical engineering

Ji Xu et al.

CHEMICAL ENGINEERING SCIENCE (2015)

Article Chemistry, Physical

Exact milestoning

Juan M. Bello-Rivas et al.

JOURNAL OF CHEMICAL PHYSICS (2015)

Article Chemistry, Physical

Contact- and distance-based principal component analysis of protein dynamics

Matthias Ernst et al.

JOURNAL OF CHEMICAL PHYSICS (2015)

Article Chemistry, Physical

Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method

Joshua L. Adelman et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis

Matthew C. Zwier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

Yinglong Miao et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

Jeffrey Comer et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

Article Chemistry, Medicinal

AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble

Badi' Abdul-Wahid et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)

Article Chemistry, Physical

WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm

Alex Dickson et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2014)

Article Chemistry, Physical

Identification of slow molecular order parameters for Markov model construction

Guillermo Perez-Hernandez et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

Christian R. Schwantes et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Using collective variables to drive molecular dynamics simulations

Giacomo Fiorin et al.

MOLECULAR PHYSICS (2013)

Review Biophysics

Biomolecular Simulation: A Computational Microscope for Molecular Biology

Ron O. Dror et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 41 (2012)

Article Chemistry, Physical

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

Levi C. T. Pierce et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Review Biology

Molecular dynamics simulations and drug discovery

Jacob D. Durrant et al.

BMC BIOLOGY (2011)

Article Chemistry, Physical

Multiple state transition interface sampling of alanine dipeptide in explicit solvent

Wei-Na Du et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

Article Chemistry, Physical

Optimizing transition interface sampling simulations

Ernesto E. Borrero et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

Article Multidisciplinary Sciences

How Fast-Folding Proteins Fold

Kresten Lindorff-Larsen et al.

SCIENCE (2011)

Review Chemistry, Multidisciplinary

Umbrella sampling

Johannes Kaestner

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)

Review Chemistry, Multidisciplinary

Metadynamics

Alessandro Barducci et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)

Editorial Material Engineering, Chemical

Historical Perspective and Current Outlook for Molecular Dynamics As a Chemical Engineering Tool

E. J. Maginn et al.

INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH (2010)

Article Chemistry, Physical

Steady-state simulations using weighted ensemble path sampling

Divesh Bhatt et al.

JOURNAL OF CHEMICAL PHYSICS (2010)

Article Chemistry, Physical

Milestoning without a Reaction Coordinate

Peter Majek et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Chemistry, Physical

Exchange Often and Properly in Replica Exchange Molecular Dynamics

Daniel J. Sindhikara et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Biochemistry & Molecular Biology

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Kresten Lindorff-Larsen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

Atomic-Level Characterization of the Structural Dynamics of Proteins

David E. Shaw et al.

SCIENCE (2010)

Review Biochemistry & Molecular Biology

A Review of Computational Methods in Materials Science: Examples from Shock-Wave and Polymer Physics

Martin O. Steinhauser et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2009)

Article Chemistry, Physical

Error and efficiency of replica exchange molecular dynamics simulations

Edina Rosta et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

Markovian milestoning with Voronoi tessellations

Eric Vanden-Eijnden et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Review Physics, Condensed Matter

Forward flux sampling for rare event simulations

Rosalind J. Allen et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2009)

Article Chemistry, Physical

Adaptive biasing force method for scalar and vector free energy calculations

Eric Darve et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

On the assumptions underlying milestoning

Eric Vanden-Eijnden et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Exchange frequency in replica exchange molecular dynamics

Daniel Sindhikara et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Mathematics, Applied

Long-time convergence of an adaptive biasing force method

Tony Lelievre et al.

NONLINEARITY (2008)

Article Physics, Multidisciplinary

Well-tempered metadynamics: A smoothly converging and tunable free-energy method

Alessandro Barducci et al.

PHYSICAL REVIEW LETTERS (2008)

Review Physics, Multidisciplinary

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

Alessandro Laio et al.

REPORTS ON PROGRESS IN PHYSICS (2008)

Article Chemistry, Physical

Umbrella sampling for nonequilibrium processes

Aryeh Warmflash et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling

Chantal Valeriani et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Materials Science, Multidisciplinary

Molecular dynamics simulations of coherent optical photon emission from shock waves in crystals

Evan J. Reed et al.

PHYSICAL REVIEW B (2007)

Article Biochemistry & Molecular Biology

Comparison of multiple amber force fields and development of improved protein backbone parameters

Viktor Hornak et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Chemistry, Physical

Forward flux sampling-type schemes for simulating rare events: Efficiency analysis

Rosalind J. Allen et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Physics, Multidisciplinary

Equilibrium free energies from nonequilibrium metadynamics

G Bussi et al.

PHYSICAL REVIEW LETTERS (2006)

Article Chemistry, Physical

Convergence of replica exchange molecular dynamics

W Zhang et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Multidisciplinary Sciences

Molecular dynamics and protein function

M Karplus et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Computer Science, Interdisciplinary Applications

Elaborating transition interface sampling methods

TS van Erp et al.

JOURNAL OF COMPUTATIONAL PHYSICS (2005)

Article Chemistry, Physical

Assessing the accuracy of metadynamics

A Laio et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Physics, Multidisciplinary

Investigating rare events by transition interface sampling

D Moroni et al.

PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS (2004)

Article Chemistry, Physical

Calculation of free energy through successive umbrella sampling

P Virnau et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Chemistry, Physical

Computing time scales from reaction coordinates by milestoning

AK Faradjian et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Chemistry, Physical

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

HW Horn et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Review Biochemistry & Molecular Biology

Molecular dynamics simulations of biomolecules

M Karplus et al.

NATURE STRUCTURAL BIOLOGY (2002)

Article Chemistry, Physical

Calculating free energies using average force

E Darve et al.

JOURNAL OF CHEMICAL PHYSICS (2001)

Article Chemistry, Physical

Modification of the generalized Born model suitable for macromolecules

A Onufriev et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2000)