Molecular dynamics for conformational sampling
Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations.
... the conformational sampling of our ...the conformational ensembles, and show that the subunit response, as observed in the oligomeric structure, is intrinsically coded in the ...
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Adaptive conformational sampling based on replicas
... current sampling of dihedral rotamers in the target replica and recording its cumulative ...The sampling scheme has been implemented and compared with different procedures for learning in the searching ...
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Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations
... simulation time, can be higher or lower than that of the cor- responding explicit-solvent simulation due to differences in how the two approximations scale with system size. The most common explicit-solvent PME ...
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Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations
... All-atom molecular dynamics simulations are widely used to study the flexibility of protein ...enhanced sampling techniques are required for simulating protein dynamics that occur on the ...
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Molecular simulation methods for conformational searches and diffusivity
... a conformational search method for explicitly solvated molecules was ...presented. Molecular conformations affect the biological activity and binding affinity of drug ...Many conformational search ...
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Conformational Fluctuations of Biomolecules Studied Using Molecular Dynamics and Enhanced Sampling
... 4.2 Introduction Chemical biology and biomedical sciences are undergoing a new era of vigorous development due to the rapid discovery of new protein targets and unveiling of their biological importance. Consequently, it ...
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On the Conformational Dynamics of DNA: A Perspective from Molecular Dynamics Simulations
... umbrella sampling 133 using a harmonic restraint that minimizes the total squared distance between the actual atoms and atoms on an idealized helix of a desired radius and ...
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Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.
... the dynamics of nucleotide-dependent conformational ...unbiased molecular dynamics (MD) simulations were restricted to characterizing fluctuations within individual nucleotide states ...
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Enhanced Sampling Methods for Molecular Dynamics Simulations of Proteins
... of conformational states accessible to a typical protein, a random walk through configuration space (even if spending a very short time in each state) would take an astronomically large amount of time to reach the ...
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A Molecular Dynamics Study of Slow Base Flipping in DNA using Conformational Flooding
... ABSTRACT Individual DNA bases are known to be able to flip out of the helical stack, providing enzymes with access to the genetic information otherwise hidden inside the helix. Consequently, base flipping is a necessary ...
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A Molecular Dynamics Study of Slow Base Flipping in DNA using Conformational Flooding
... ABSTRACT Individual DNA bases are known to be able to flip out of the helical stack, providing enzymes with access to the genetic information otherwise hidden inside the helix. Consequently, base flipping is a necessary ...
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Sampling molecular conformations and dynamics in a multiuser virtual reality framework
... interactive molecular dynamics in a multiuser virtual reality (VR) environment, combining rigorous cloud-mounted atomistic physics simulations with commodity VR hardware, which we have made accessible to ...
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Molecular dynamics study of conformational changes in human serum albumin by binding of fatty acids
... each sampling was not fully converged as described previously, the results suggest that increasing the number of MYR binding to HSA causes the increase in the ratio of entropic cost in the binding free ...
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A Virtual Reality Environment for Interactive Molecular Dynamics Simulations of Complex Conformational Changes in Proteins
... MD sampling per minute of real time for a modestly sized protein solvated in a box ...Such sampling time is several orders of magnitude below the timescale of protein folding or large scale ...
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Molecular Dynamics Simulations Towards The Understanding of the Cis Trans Isomerization of Proline As A Conformational Switch For The Regulation of Biological Processes
... impoverishment phenomena occurs when after several iterations, all the particles are generated by multiplying a small number of particles ( because these particles have dominant weight or because other particles have a ...
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Macroscopic Electrostatic Force in Molecular Conformational Dynamics
... “Under the combined influence of electric field generated by solute charges and their polarization in the surrounding medium which is electrostatic neutral, an additional potential energ[r] ...
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Some remarks on sampling methods in Molecular Dynamics
... Nos´e-Hoover dynamics have been proposed (see [14] for more de- ...chain dynamics [31, 51, 56, ...Hamiltonian dynamics, like the Nos´e-Poincar´e method [8] and the Recursive Multiple Thermostats ...
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Some connections between importance sampling and enhanced sampling methods in molecular dynamics
... set molecular dynamics and enhanced sampling in the frame- work of mathematical probability ...portance sampling and showed that enhanced sampling can be viewed as im- portance ...
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Some connections between importance sampling and enhanced sampling methods in molecular dynamics
... In molecular dynamics, the above approach is realized by exploiting the known correspondences between the energy function that determines the Boltzmann-Gibbs distribution and the associated distribution µ ...
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Importance sampling for metastable dynamical systems in molecular dynamics
... of sampling effort has to be used to explore the state space of the system to get this relevant ...the sampling of thermodynamic quantities this is necessary because the stationary distribution which ...
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