☆ 4.4 Article

Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer

JOURNAL OF COMPUTATIONAL CHEMISTRY (2023)

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, Multidisciplinary

Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency

Daiki Fukuhara et al.

Summary: In the replica-permutation method, the temperature transition probability depends on how the list of combinations is created. Sequential assignment of combinations to state labels can cause a decrease in transition probabilities, especially for large replica indices. By randomly assigning the combinations to state labels, this problem can be solved and the sampling efficiency can be improved.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2023)

添加到收藏夹

Article Chemistry, Physical

Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments

Daiki Fukuhara et al.

Summary: In this study, we propose a improved method called replica permutation with solute tempering (RPST) by combining replica-permutation method (RPM) and replica exchange with solute tempering (REST). RPST achieves more efficient temperature transitions and reduces the number of replicas compared to other methods. By applying RPST, REST, RPM, and REM to simulate two amyloid-beta(16-22) peptides, we observed that RPST requires fewer replicas to simulate frequent random walks in temperature and conformational spaces, and it successfully captures the dimerization process of the peptides.

JOURNAL OF CHEMICAL PHYSICS (2022)

添加到收藏夹

Article Computer Science, Interdisciplinary Applications

LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Aidan P. Thompson et al.

Summary: LAMMPS, a classical molecular dynamics simulator released as an open source code in 2004, has gained popularity for its wide variety of particle interaction models, platform compatibility, and user control over simulation details. With contributions from numerous developers, it has grown from 50,000 lines of code to a million today, showcasing new capabilities like dynamic load balancing and quantum-accuracy machine learning interatomic potentials.

COMPUTER PHYSICS COMMUNICATIONS (2022)

添加到收藏夹

Article Biology

The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein

Hisham M. Dokainish et al.

Summary: The Spike protein plays a crucial role in neutralization and vaccine development for SARS-CoV-2. Its inherent flexibility provides essential information for designing antiviral drugs and vaccines.

ELIFE (2022)

添加到收藏夹

Article Biochemistry & Molecular Biology

Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling

Hisham M. Dokainish et al.

Summary: The study proposes a new approach, gREST_SSCR, for exploring open-closed conformational changes in multidomain proteins. By using this method, a wider conformational space is reached compared to conventional MD, while maintaining the stability of protein domains.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

添加到收藏夹

Article Chemistry, Multidisciplinary

New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems

Jaewoon Jung et al.

Summary: This paper addresses the high performance extreme-scale molecular dynamics algorithm in the GENESIS software for cellular-scale MD simulations, achieving a performance of 8.30 ns/day on Fugaku supercomputer with a system containing 1.6 billion atoms, extending the size and time of MD simulations.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2021)

添加到收藏夹

Article Multidisciplinary Sciences

High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme

Rajeswari Appadurai et al.

Summary: The study introduces a parallel-tempering method that utilizes accelerated water dynamics for efficient and accurate conformational sampling across a wide variety of proteins, demonstrating successful application to large metamorphic proteins and highly disordered proteins with good fit to experimental data.

NATURE COMMUNICATIONS (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models

Xiaowei Wang et al.

Summary: This article introduces a protocol specifically tailored for studying functional conformational changes of proteins, emphasizing the importance of selecting proper molecular features to describe the slowest timescales of interest. The recommendation of spectral oASIS and deep learning methods for automatic feature selection and discovering collective variables is provided. Through case studies on DNA repair enzymes and RNA polymerases, recent applications of MSMs in elucidating molecular mechanisms of functional conformational changes are reviewed, along with discussions on the challenges and future prospects in constructing MSMs for studying protein conformational changes.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2021)

添加到收藏夹

Article Chemistry, Physical

Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems

Jaewoon Jung et al.

Summary: Recent years have seen an advancement in molecular dynamics (MD) simulations with larger time steps using the hydrogen-mass-repartitioning (HMR) scheme. By optimizing HMR scaling factors and incorporating accurate temperature/pressure evaluations, stable and reliable MD trajectories with larger time steps have been achieved, providing more efficiency in comparison to conventional methods.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Reduced efficacy of a Src kinase inhibitor in crowded protein solution

Kento Kasahara et al.

Summary: The cell is crowded with proteins and other biomolecules, and the binding dynamics of an inhibitor with c-Src kinase can change in crowded environments compared to dilute solutions, potentially due to local conformational shifts in c-Src kinase. The presence of crowders like bovine serum albumins can reduce the efficacy of the inhibitor in experimental assays, highlighting the importance of understanding ligand binding pathways in crowded cellular environments.

NATURE COMMUNICATIONS (2021)

添加到收藏夹

Article Chemistry, Physical

The Unfolding Journey of Superoxide Dismutase 1 Barrels under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions with Crowders

Stepan Timr et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2020)

添加到收藏夹

Article Chemistry, Medicinal

Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST plus FEP Method

Hiraku Oshima et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

添加到收藏夹

Article Chemistry, Physical

Scalable molecular dynamics on CPU and GPU architectures with NAMD

James C. Phillips et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

添加到收藏夹

Article Chemistry, Physical

Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step

Jaewoon Jung et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

添加到收藏夹

Article Chemistry, Multidisciplinary

Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations

Jaewoon Jung et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2019)

添加到收藏夹

Article Chemistry, Medicinal

De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

Ai Niitsu et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)

添加到收藏夹

Article Multidisciplinary Sciences

Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape

Suyong Re et al.

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

添加到收藏夹

Article Chemistry, Physical

Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step

Jaewoon Jung et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

添加到收藏夹

Article Chemistry, Physical

Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation

Jaewoon Jung et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

添加到收藏夹

Article Chemistry, Physical

Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations

Motoshi Kamiya et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

添加到收藏夹

Article Chemistry, Multidisciplinary

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

Chigusa Kobayashi et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)

添加到收藏夹

Article Biochemical Research Methods

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

Peter Eastman et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

添加到收藏夹

Article Computer Science, Interdisciplinary Applications

Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

Jaewoon Jung et al.

COMPUTER PHYSICS COMMUNICATIONS (2016)

添加到收藏夹

Article Chemistry, Physical

Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations

Jaewoon Jung et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

添加到收藏夹

Article Chemistry, Physical

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

Chad W. Hopkins et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

添加到收藏夹

Article Biochemical Research Methods

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology

Michael Feig et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2015)

添加到收藏夹

Article Chemistry, Multidisciplinary

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Jaewoon Jung et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2015)

添加到收藏夹

Article Chemistry, Physical

Perspective: Markov models for long-timescale biomolecular dynamics

C. R. Schwantes et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

添加到收藏夹

Article Chemistry, Physical

Prediction of Ligand Binding Affinity by the Combination of Replica-Exchange Method and Double-Decoupling Method

Yuko Okamoto et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

添加到收藏夹

Article Chemistry, Physical

Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique

Bastien Loubet et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

添加到收藏夹

Article Chemistry, Multidisciplinary

New Faster CHARMM Molecular Dynamics Engine

Antti-Pekka Hynninen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)

添加到收藏夹

Article Chemistry, Multidisciplinary

Midpoint Cell Method for Hybrid ( MPI1OpenMP) Parallelization of Molecular Dynamics Simulations

Jaewoon Jung et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)

添加到收藏夹

Article Biochemical Research Methods

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Sander Pronk et al.

BIOINFORMATICS (2013)

添加到收藏夹

Article Chemistry, Physical

Replica-Permutation Method with the Suwa-Todo Algorithm beyond the Replica-Exchange Method

Satoru G. Itoh et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

添加到收藏夹

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Romelia Salomon-Ferrer et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

添加到收藏夹

Article Chemistry, Multidisciplinary

Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions

Ryuhei Harada et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

添加到收藏夹

Article Chemistry, Physical

Improved Replica Exchange Method for Native-State Protein Sampling

Samuel L. C. Moors et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

添加到收藏夹

Article Chemistry, Multidisciplinary

On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS

Tsuyoshi Terakawa et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

添加到收藏夹

Correction Chemistry, Physical

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2) (vol 115, pg 9431, 2011)

Lingle Wang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2011)

添加到收藏夹

Article Chemistry, Physical

Replica-exchange method in van der Waals radius space: Overcoming steric restrictions for biomolecules

Satoru G. Itoh et al.

JOURNAL OF CHEMICAL PHYSICS (2010)

添加到收藏夹

Review Chemistry, Multidisciplinary

CHARMM: The Biomolecular Simulation Program

B. R. Brooks et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

添加到收藏夹

Article Chemistry, Physical

Statistically optimal analysis of samples from multiple equilibrium states

Michael R. Shirts et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

添加到收藏夹

Article Chemistry, Physical

Replica exchange with solute tempering: Efficiency in large scale systems

Xuhui Huang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

添加到收藏夹

Article Chemistry, Physical

Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

Adrian E. Roitberg et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

添加到收藏夹

Article Chemistry, Physical

The midpoint method for parallelization of particle simulations

Kevin J. Bowers et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

添加到收藏夹

Review Chemistry, Multidisciplinary

Scalable molecular dynamics with NAMD

JC Phillips et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

添加到收藏夹

Article Multidisciplinary Sciences

Replica exchange with solute tempering: A method for sampling biological systems in explicit water

P Liu et al.

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

添加到收藏夹

Article Chemistry, Physical

Combination of the replica-exchange Monte Carlo method and the reference interaction site model theory for simulating a peptide molecule in aqueous solution

A Mitsutake et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2004)

添加到收藏夹

Article Chemistry, Physical

Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test

A Mitsutake et al.

JOURNAL OF CHEMICAL PHYSICS (2003)

添加到收藏夹

Article Biophysics

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

YM Rhee et al.

BIOPHYSICAL JOURNAL (2003)

添加到收藏夹

Article Biochemistry & Molecular Biology

Hybrid Monte Carlo with multidimensional replica exchanges:: Conformational equilibria of the hypervariable reigons of a llamma VHH antibody domain

MK Fenwick et al.

BIOPOLYMERS (2003)

添加到收藏夹

Article Chemistry, Physical

On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction

H Fukunishi et al.

JOURNAL OF CHEMICAL PHYSICS (2002)

添加到收藏夹

Article Chemistry, Physical

Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble

T Okabe et al.

CHEMICAL PHYSICS LETTERS (2001)

添加到收藏夹

Article Chemistry, Physical

Multidimensional replica-exchange method for free-energy calculations

Y Sugita et al.

JOURNAL OF CHEMICAL PHYSICS (2000)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.