Dmitry Nerukh
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View article: Fitness Effect of the Isoniazid Resistance Mutation S315T of the Catalase-Peroxidase Enzyme KatG of <i>Mycobacterium tuberculosis</i>
Fitness Effect of the Isoniazid Resistance Mutation S315T of the Catalase-Peroxidase Enzyme KatG of <i>Mycobacterium tuberculosis</i> Open
The mutation S315T of the catalase–peroxidase (CP) protein KatG of Mycobacterium tuberculosis is the most common mutation that confers resistance to the prodrug isoniazid. Here, we reconstruct its evolutionary history in 145 whole-genome s…
View article: The Multiscale Hybrid Method with a Localized Constraint. II. Hybrid Equations of Motion Based on Variational Principles
The Multiscale Hybrid Method with a Localized Constraint. II. Hybrid Equations of Motion Based on Variational Principles Open
A multiscale modelling framework that employs molecular dynamics and hydrodynamics principles has been developed to describe the dynamics of hybrid particles. Based on the principle of least action, the equations of motion for hybrid parti…
View article: The Multiscale Hybrid Method with a Localized Constraint. I. A Modified Control Volume Function for the Hybridized Mass and Momentum Equations
The Multiscale Hybrid Method with a Localized Constraint. I. A Modified Control Volume Function for the Hybridized Mass and Momentum Equations Open
A new hybrid multiscaling model has been developed on the basis of the modified control volume function. Following the two-phase analogy of the same substance, the continuum and particle representations are coupled together in the framewor…
View article: Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density
Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density Open
We, for the first time, reconstruct from the published incomplete cryo-EM density a complete MS2 virus at atomistic resolution, that is, the capsid with the genome, and validate the result by all-atom molecular dynamics with explicit water.
View article: Protein-ligand dissociation rate constant from all-atom simulation
Protein-ligand dissociation rate constant from all-atom simulation Open
Dissociation of a ligand isoniazid from a protein catalase was investigated using all-atom Molecular Dynamics (MD) simulations. Random Acceleration MD (τ-RAMD) was used where a random artificial force applied to the ligand facilitates its …
View article: Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly
Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly Open
The GH-loop located near the icosahedral 3-fold axes of symmetry regulates Porcine Circovirus 2 capsid assembly.
View article: Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation
Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation Open
Tumor Necrosis Factor-alpha (TNF-α), a multifunctional cytokine responsible for providing resistance against infections, inflammation, and cancers. TNF-α has emerged as a promising drug target against several autoimmune and inflammatory di…
View article: MS2 bacteriophage capsid studied using all-atom molecular dynamics
MS2 bacteriophage capsid studied using all-atom molecular dynamics Open
The all-atom model of an MS2 bacteriophage particle without its genome (the capsid) was built using high-resolution cryo-electron microscopy (EM) measurements for initial conformation. The structural characteristics of the capsid and the d…
View article: Supplementary material from "MS2 bacteriophage capsid studied using all-atom molecular dynamics"
Supplementary material from "MS2 bacteriophage capsid studied using all-atom molecular dynamics" Open
The all-atom model of an MS2 bacteriophage particle without its genome (the capsid) was built using high-resolution cryo-EM measurements for initial conformation. The structural characteristics of the capsid and the dynamics of the surroun…
View article: All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid’s Stability
All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid’s Stability Open
Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of i…
View article: Run Input file for energy minimization of capsid(7f-3.tpr)
Run Input file for energy minimization of capsid(7f-3.tpr) Open
Run Input file for energy minimization of capsid
View article: trajectory files of MD simulation after 100ps at 200K(9f-3_new.xtc)
trajectory files of MD simulation after 100ps at 200K(9f-3_new.xtc) Open
trajectory files of MD simulation after 100ps at 200K
View article: Run Input file for MD simulation after 100ps at 200K (9f-3.tpr)
Run Input file for MD simulation after 100ps at 200K (9f-3.tpr) Open
Run Input file for MD simulation after 100ps at 200K
View article: Structure file of capsid after energy minimization (7f-3.gro )
Structure file of capsid after energy minimization (7f-3.gro ) Open
Structure file of capsid after energy minimization
View article: structure file of MD simulation after 100ps at 200K (9f-3.gro)
structure file of MD simulation after 100ps at 200K (9f-3.gro) Open
structure file of MD simulation after 100ps at 200K
View article: Trajectory file of energy minimization of capsid(7f-3.trr)
Trajectory file of energy minimization of capsid(7f-3.trr) Open
Trajectory file of energy minimization of capsid