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all atom molecular dynamics flexible fitting mdff  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc all atom molecular dynamics flexible fitting mdff
    All Atom Molecular Dynamics Flexible Fitting Mdff, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/dynamics+flexible+fitting+(mdff)/fitting+flexible/pm25389565__ja506385p_si_001-2-10-11
    Average 86 stars, based on 1 article reviews
    all atom molecular dynamics flexible fitting mdff - by Bioz Stars, 2026-09
    86/100 stars

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    other:

    Article Title: Bacterial tubulin TubZ-Bt transitions between a two-stranded intermediate and a four-stranded filament upon GTP hydrolysis
    Article Snippet: Subtle adjustments to the structure of the loop between H6 and H7, and H11 ( and Fig. S4 C ) were made using Molecular Dynamics Flexible Fitting (MDFF) ( 23 ).

    Article Title: Iterative Molecular Dynamics – Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities
    Article Snippet: Molecular dynamics flexible fitting (MDFF) MDFF simulations were run on the starting models in the presence of membrane and in solution depending on the type of protein used 69 .

    Article Title: Three-Dimensional Asymmetric Reconstruction of Tailed Bacteriophage
    Article Snippet: Molecular dynamics based packages such as MDFF (molecular dynamics flexible fitting; Trabuco et al ., 2008 ) adjust the crystal structure in a physically reasonable way and even show a potential trajectory between conformations.

    Article Title: Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model
    Article Snippet: Molecular dynamics flexible fitting ( MDFF ) uses prepared structures [ , ], input parameters [ ], or interactive input by users [ , ].

    Article Title: Structure of the 70S ribosome from human pathogen Staphylococcus aureus
    Article Snippet: Molecular dynamics flexible fitting (MDFF; ( )) was performed for the complete 70S ribosome in VMD v. 1.9.2 , using NAMD v. 2 (gscale 0.3, numsteps 500 000, minsteps 2000) ( ).

    Article Title: De novo main-chain modeling for EM maps using MAINMAST
    Article Snippet: Finally, the full-atom models are refined using Molecular Dynamics Flexible Fitting (MDFF)21, a molecular dynamics-based method, and selected according to the scoring function implemented in MDFF.” Also along similar lines, in Fig 4, "2.9 Å (EMD-6478).

    Article Title: A Pseudo-Atomic Model of the COPII Cage Obtained from CryoEM and Mass Spectrometry Analyses
    Article Snippet: The flexible fitting processes were performed by use of Molecular Dynamics Flexible Fitting (MDFF) as described in .

    Solvent:

    Article Title: Structure of human TRPM8 channel.
    Article Snippet: For the preparation of Supplementary Movie 1, 3D Variability analysis was performed in cryoSPARC and selected components were reconstructed into three frames with 3D Variability Display tool. .. Next, HsTRPM8 atomic model was fitted into these reconstructions by using a molecular dynamics flexible fitting (MDFF)39 simulation with explicit solvent in VMD-1.9.340 and NAMD v2.1241. ..



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    The atomistic representation of a functional RTC monomer (A) with the RNA (red), extended to the active site of the other nsp14–10 unit of the opposite monomer (nsp14B - orange), and the exit site on the helicase of the same monomer (nsp13–2A). The mechanism of RNA unwinding using <t>non-equilibrium</t> <t>molecular</t> dynamics simulations starting from the initial structure as captured in 7EGQ (B-left), to the final structure (B-right). The RNA backbone is restrained with an <t>mdff</t> grid, represented in a grey mesh, while using colvars to pull the strands to the active sites on the protein. This is an unprecedented simulation of the mechanism of RNA unwinding which can give significant insight into the RTC function.
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    The atomistic representation of a functional RTC monomer (A) with the RNA (red), extended to the active site of the other nsp14–10 unit of the opposite monomer (nsp14B - orange), and the exit site on the helicase of the same monomer (nsp13–2A). The mechanism of RNA unwinding using non-equilibrium molecular dynamics simulations starting from the initial structure as captured in 7EGQ (B-left), to the final structure (B-right). The RNA backbone is restrained with an mdff grid, represented in a grey mesh, while using colvars to pull the strands to the active sites on the protein. This is an unprecedented simulation of the mechanism of RNA unwinding which can give significant insight into the RTC function.

    Journal: The international journal of high performance computing applications

    Article Title: Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

    doi: 10.1177/10943420221113513

    Figure Lengend Snippet: The atomistic representation of a functional RTC monomer (A) with the RNA (red), extended to the active site of the other nsp14–10 unit of the opposite monomer (nsp14B - orange), and the exit site on the helicase of the same monomer (nsp13–2A). The mechanism of RNA unwinding using non-equilibrium molecular dynamics simulations starting from the initial structure as captured in 7EGQ (B-left), to the final structure (B-right). The RNA backbone is restrained with an mdff grid, represented in a grey mesh, while using colvars to pull the strands to the active sites on the protein. This is an unprecedented simulation of the mechanism of RNA unwinding which can give significant insight into the RTC function.

    Article Snippet: To speed up these empirical studies, instead of the all-atom representation, the protein was represented by a molecular dynamics flexible fitting mdff grid map exerting a repulsive gridForce ( Trabuco et al., 2009 ).

    Techniques: Functional Assay

    Summary of AAMD simulations.

    Journal: The international journal of high performance computing applications

    Article Title: Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

    doi: 10.1177/10943420221113513

    Figure Lengend Snippet: Summary of AAMD simulations.

    Article Snippet: To speed up these empirical studies, instead of the all-atom representation, the protein was represented by a molecular dynamics flexible fitting mdff grid map exerting a repulsive gridForce ( Trabuco et al., 2009 ).

    Techniques: Sampling