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Targeting Electrostatic Interactions in Accelerated Molecular Dynamics with Application to Protein Partial Unfolding

https://doi.org/10.1021/ct501090y
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Effect of a buried ion pair in the hydrophobic core of a protein: An insight from constant pH molecular dynamics study
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Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
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The Amber biomolecular simulation programs
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Comparison of multiple Amber force fields and development of improved protein backbone parameters
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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VMD: Visual molecular dynamics
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Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization
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Architecture and Membrane Interactions of the EGF Receptor
inferredcites →https://doi.org/10.1016/j.jmb.2013.04.030openalex-snapshot
pH-Triggered Conformational Switching of the Diphtheria Toxin T-Domain: The Roles of N-Terminal Histidines
inferredcites →https://doi.org/10.1016/s0009-2614(99)01123-9openalex-snapshot
Replica-exchange molecular dynamics method for protein folding
inferredcites →https://doi.org/10.1021/ct200615kopenalex-snapshot
Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/ct300284copenalex-snapshot
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
inferredcites →https://doi.org/10.1021/ct400314yopenalex-snapshot
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
inferredcites →https://doi.org/10.1021/ct500090qopenalex-snapshot
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
inferredcites →https://doi.org/10.1021/ct800160qopenalex-snapshot
Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations
inferredcites →https://doi.org/10.1021/ct800250mopenalex-snapshot
Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration
inferredcites →https://doi.org/10.1021/ct9005294openalex-snapshot
Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics
inferredcites →https://doi.org/10.1021/jp401587eopenalex-snapshot
Population Based Reweighting of Scaled Molecular Dynamics
inferredcites →https://doi.org/10.1021/jz500179aopenalex-snapshot
Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent
inferredcites →https://doi.org/10.1039/c1cp22100kopenalex-snapshot
Studying functional dynamics in bio-molecules using accelerated molecular dynamics
inferredcites →https://doi.org/10.1063/1.1472510openalex-snapshot
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
inferredcites →https://doi.org/10.1063/1.1755656openalex-snapshot
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
inferredcites →https://doi.org/10.1063/1.2789432openalex-snapshot
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
inferredcites →https://doi.org/10.1063/1.464397openalex-snapshot
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
inferredcites →https://doi.org/10.1063/1.470117openalex-snapshot
A smooth particle mesh Ewald method
inferredcites →https://doi.org/10.1073/pnas.0811223106openalex-snapshot
A conserved protonation-dependent switch controls drug binding in the Abl kinase
inferredcites →https://doi.org/10.1073/pnas.1112143109openalex-snapshot
Folding helical proteins in explicit solvent using dihedral-biased tempering
inferredcites →https://doi.org/10.1073/pnas.1215166109openalex-snapshot
Correction for Zhang and Ma, Folding helical proteins in explicit solvent using dihedral-biased tempering
inferredcites →https://doi.org/10.1073/pnas.1304749110openalex-snapshot
Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
inferredcites →https://doi.org/10.1088/1749-4699/4/1/015002openalex-snapshot
Implementation of accelerated molecular dynamics in NAMD
inferredcites →https://doi.org/10.1126/science.1142824openalex-snapshot
Mechanism of Na + /H + Antiporting
inferredcites →https://doi.org/10.1126/science.1187409openalex-snapshot
Atomic-Level Characterization of the Structural Dynamics of Proteins
inferredcites →https://doi.org/10.1201/9780203833445openalex-snapshot
Molecular Biology of the Cell
inferredcites →https://doi.org/10.1371/journal.pone.0032131openalex-snapshot
Systematic Validation of Protein Force Fields against Experimental Data

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inferred← citeshttps://doi.org/10.1016/j.intimp.2023.110725openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.micpath.2022.105670openalex-snapshot
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