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dynamics flexible fitting mdff grid map  (Molecular Dynamics Inc)

 
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    Structured Review

    Molecular Dynamics Inc dynamics flexible fitting mdff grid map
    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.
    Dynamics Flexible Fitting Mdff Grid Map, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/dynamics+flexible+fitting+mdff+grid+map/pmc10923581-249-18-17?v=Molecular+Dynamics+Inc
    Average 90 stars, based on 1 article reviews
    dynamics flexible fitting mdff grid map - by Bioz Stars, 2026-07
    90/100 stars

    Images

    1) Product Images from "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"

    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

    Journal: The international journal of high performance computing applications

    doi: 10.1177/10943420221113513

    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.
    Figure Legend 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.

    Techniques Used: Functional Assay

    Summary of AAMD simulations.
    Figure Legend Snippet: Summary of AAMD simulations.

    Techniques Used: Sampling



    Similar Products

    dynamics flexible fitting mdff grid map  (Molecular Dynamics Inc)
    90
    Molecular Dynamics Inc dynamics flexible fitting mdff grid map
    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.
    Dynamics Flexible Fitting Mdff Grid Map, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/dynamics+flexible+fitting+mdff+grid+map/pmc10923581-249-18-17?v=Molecular+Dynamics+Inc
    Average 90 stars, based on 1 article reviews
    dynamics flexible fitting mdff grid map - by Bioz Stars, 2026-07
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    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