Biophysics

Molecular Modeling at the Atomic Scale: Methods and by Ruhong Zhou

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By Ruhong Zhou

''Developments in molecular modeling from experimental and computational innovations have enabled quite a lot of organic functions. This well timed precis displays the hot advances in bridging novel algorithms and excessive functionality computing with characterization of significant organic techniques, equivalent to folding dynamics of key proteins. It encompasses the views of major specialists in this transformation Read more...

summary: ''Developments in molecular modeling from experimental and computational suggestions have enabled quite a lot of organic purposes. This well timed precis displays the hot advances in bridging novel algorithms and excessive functionality computing with characterization of significant organic tactics, equivalent to folding dynamics of key proteins. It encompasses the views of best specialists in this transformation in molecular biology, illustrating with cutting-edge examples how molecular modeling methods are being utilized to serious questions in smooth quantitative biology''--Provided by means of writer

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1 Hydrophobic-Aided Replica Exchange Hydrophobic in aided replica exchange (HAREM) [79] is a variant of Hamiltonian REM, which is inspired by the observation that the increase in the protein hydrophobicity can greatly accelerate the protein hydrophobic collapse [80–82]. Previous studies show that protein hydrophobicity can be tuned by scaling the protein–water attractive interactions [80–82]. For example, Zhou et al. [81] observed that the collapse of the two domains of the BphC enzyme can be accelerated by around 10 times when the electrostatic protein–water interactions (Eelec) are turned off.

They have further selected a number of intermediate replicas between the coarse-grained model and atomistic model to ensure a reasonable acceptance ratio between the neighboring replicas. Liu and Voth [90] 27 28 Introduction to Molecular Dynamics and Enhanced Sampling Algorithms adopted a rather different approach using only two replicas in their method: one at atomistic resolution and the other at coarse-grained resolution. They allow the atomistic conformation constructed from the coarse-grained resolution replica to be fully relaxed before attempting the exchange by applying the smart walking algorithm developed by Zhou and Berne [91].

Other box shapes such as the rhombic dodecahedron and truncated octahedron may be more suitable for the simulations of the spherical macromolecules, since these two shapes are closer to a sphere and thus require a smaller number of solvent molecules. 4 Neighbor List With periodic boundary conditions, one can mimic the infinite system using a finite simulation box. For certain configurations, one would need to calculate the vdW and electrostatic interactions between infinite numbers of pairs of atoms, which is impossible.

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