Cargando…

Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension

[Image: see text] Replica exchange (REX) is a powerful computational tool for overcoming the quasi-ergodic sampling problem of complex molecular systems. Recently, several multidimensional extensions of this method have been developed to realize exchanges in both temperature and biasing potential sp...

Descripción completa

Detalles Bibliográficos
Autores principales:	Yang, Mingjun, Huang, Jing, MacKerell, Alexander D.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	American Chemical Society 2015
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463548/ https://www.ncbi.nlm.nih.gov/pubmed/26082676 http://dx.doi.org/10.1021/acs.jctc.5b00243

Ejemplares similares

Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments
por: Patel, Dhilon S., et al.
Publicado: (2014)

Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential
por: Ostermeir, Katja, et al.
Publicado: (2017)

Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods
por: Roe, Daniel R., et al.
Publicado: (2014)

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
por: Arrar, Mehrnoosh, et al.
Publicado: (2012)

Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange
por: Liu, Yang, et al.
Publicado: (2020)

Hamiltonian-Reservoir Replica Exchange and Machine Learning Potentials for Computational Organic Chemistry
por: Fabregat, Raimon, et al.
Publicado: (2020)

Conformational Heterogeneity of the HIV Envelope Glycan Shield
por: Yang, Mingjun, et al.
Publicado: (2017)

Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations?
por: Procacci, Piero
Publicado: (2022)

Enhanced Conformational Sampling of Nanobody CDR H3 Loop by Generalized Replica-Exchange with Solute Tempering
por: Higashida, Ren, et al.
Publicado: (2021)

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
por: Gil-Ley, Alejandro, et al.
Publicado: (2015)

Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations
por: Han, Nanyu, et al.
Publicado: (2013)

Differential Impact of the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) on DNA Conformational Properties
por: Savelyev, Alexey, et al.
Publicado: (2014)

Correction to Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
por: Gil-Ley, Alejandro, et al.
Publicado: (2015)

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering
por: Cole, Daniel J., et al.
Publicado: (2014)

Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange
por: Markthaler, Daniel, et al.
Publicado: (2022)

A Hamiltonian Replica Exchange Molecular Dynamics (MD) Method for the Study of Folding, Based on the Analysis of the Stabilization Determinants of Proteins
por: Meli, Massimiliano, et al.
Publicado: (2013)

Conformational Ensembles of α-Synuclein Derived Peptide with Different Osmolytes from Temperature Replica Exchange Sampling
por: Jamal, Salma, et al.
Publicado: (2017)

Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant
por: Iwai, Ryosuke, et al.
Publicado: (2018)

Characterization of Mg(2+) Distributions around RNA in Solution
por: Lemkul, Justin A., et al.
Publicado: (2016)

Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft
por: Guvench, Olgun, et al.
Publicado: (2007)

Hamiltonian Truncation with Larger Dimensions
por: Elias Miró, Joan
Publicado: (2022)

Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations
por: Lakkaraju, Sirish Kaushik, et al.
Publicado: (2014)

Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent
por: Kannan, S, et al.
Publicado: (2011)

Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase
por: Re, Suyong, et al.
Publicado: (2018)

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering
por: Huang, Kun, et al.
Publicado: (2014)

Influence of Mg(2+) Distribution on the Stability of Folded States of the Twister Ribozyme Revealed Using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced Sampling
por: Sengul, Mert Y., et al.
Publicado: (2023)

Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations
por: Voronin, Arthur, et al.
Publicado: (2020)

Zebrafish response to a robotic replica in three dimensions
por: Ruberto, Tommaso, et al.
Publicado: (2016)

Exchanging Replicas with Unequal Cost, Infinitely and Permanently
por: Roet, Sander, et al.
Publicado: (2022)

Accelerating Solvent Dynamics with Replica Exchange for Improved Free Energy Sampling
por: Darkins, Robert, et al.
Publicado: (2023)

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation
por: Guvench, Olgun, et al.
Publicado: (2009)

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field
por: Savelyev, Alexey, et al.
Publicado: (2014)

Exploring the binding pathways of the 14-3-3ζ protein: Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints
por: Nagy, Gabor, et al.
Publicado: (2017)

Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica—Exchange Molecular Dynamics Simulations
por: Kannan, Srinivasaraghavan, et al.
Publicado: (2009)

Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock
por: Zhang, Zhe, et al.
Publicado: (2013)

Realizing tight-binding Hamiltonians using site-controlled coupled cavity arrays
por: Saxena, Abhi, et al.
Publicado: (2023)

Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis
por: Banavali, Nilesh K., et al.
Publicado: (2009)

Do Halogen–Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand–Protein Binding?
por: Lin, Fang-Yu, et al.
Publicado: (2017)

Contributions and competition of Mg(2+) and K(+) in folding and stabilization of the Twister ribozyme
por: Kognole, Abhishek A., et al.
Publicado: (2020)

Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator
por: Patel, Dhilon S., et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_bint1meug8g9h020940mmm52f2