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dynamics flexible fitting (mdff) approach  (Molecular Dynamics Inc)

 
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    Structured Review

    Molecular Dynamics Inc dynamics flexible fitting (mdff) approach
    Morph from the LPF ADP MDFF model to the LPF rigor MDFF model. To generate this morph, the ADP and rigor density maps were aligned, then their corresponding atomistic models were rigid body fit into the aligned maps. Myosin, magenta, three actin subunits, varying shades of blue.
    Dynamics Flexible Fitting (Mdff) Approach, 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+%28mdff%29+approach/pmc05762158-74-14-12?v=Molecular+Dynamics+Inc
    Average 90 stars, based on 1 article reviews
    dynamics flexible fitting (mdff) approach - by Bioz Stars, 2026-07
    90/100 stars

    Images

    1) Product Images from "Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity"

    Article Title: Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity

    Journal: eLife

    doi: 10.7554/eLife.31125

    Morph from the LPF ADP MDFF model to the LPF rigor MDFF model. To generate this morph, the ADP and rigor density maps were aligned, then their corresponding atomistic models were rigid body fit into the aligned maps. Myosin, magenta, three actin subunits, varying shades of blue.
    Figure Legend Snippet: Morph from the LPF ADP MDFF model to the LPF rigor MDFF model. To generate this morph, the ADP and rigor density maps were aligned, then their corresponding atomistic models were rigid body fit into the aligned maps. Myosin, magenta, three actin subunits, varying shades of blue.

    Techniques Used:

    Morph from the ADP to rigor reconstruction, low-pass filtered at 7.5 Å focusing on the myosin VI nucleotide binding cleft with density corresponding to ADP nucleotide colored orange (left panel). To generate this morph, density maps aligned to each other. Right panel includes the LPF rigor MDFF model rigid body fit into the rigor density map.
    Figure Legend Snippet: Morph from the ADP to rigor reconstruction, low-pass filtered at 7.5 Å focusing on the myosin VI nucleotide binding cleft with density corresponding to ADP nucleotide colored orange (left panel). To generate this morph, density maps aligned to each other. Right panel includes the LPF rigor MDFF model rigid body fit into the rigor density map.

    Techniques Used:

    Morphs from actin alone to ADP, ADP to rigor, and rigor to actin alone focusing on the H-plug (red) and D-loop (orange). Right panels: Morphs of density maps, low-pass filtered to 7.5 Å and aligned to each other. Left panels: Morphs between backbone-averaged HR MDFF models. To generate the morphs of atomistic models, the density maps were aligned, then their corresponding atomistic models were rigid-body fit into the aligned maps.
    Figure Legend Snippet: Morphs from actin alone to ADP, ADP to rigor, and rigor to actin alone focusing on the H-plug (red) and D-loop (orange). Right panels: Morphs of density maps, low-pass filtered to 7.5 Å and aligned to each other. Left panels: Morphs between backbone-averaged HR MDFF models. To generate the morphs of atomistic models, the density maps were aligned, then their corresponding atomistic models were rigid-body fit into the aligned maps.

    Techniques Used:

    Morph between the backbone-averaged HR MDFF actin alone, ADP, and rigor models. Morphs generated as in <xref ref-type=Video 6 . " title="Morph between the backbone-averaged HR MDFF actin alone, ADP, and rigor models. Morphs" property="contentUrl" width="100%" height="100%"/>
    Figure Legend Snippet: Morph between the backbone-averaged HR MDFF actin alone, ADP, and rigor models. Morphs generated as in Video 6 .

    Techniques Used:

    Morph between indicated states of the myosin VI mechanochemical cycle, aligned in the reference from of the actin filament. To generate this morph, the full ADP and rigor density maps were aligned, and then the LPF ADP MDFF and LPF rigor MDFF models were rigid body fit into their corresponding densities. The grafted lever arm models were then superimposed on the LPF MDFF models using overlapping Cα coordinates. For the Pre-Powerstroke (2V26) and PiR (4PFO) states, the X-ray structures were superimposed on the LPF ADP MDFF model based on the Cα coordinates of the full motor domain. For the post-rigor (2VAS) state, the x-ray structure was superimposed on the LPF rigor MDFF model based on the Cα coordinates of the full motor domain. The lever arms of crystal structures were extended in a manner analogous to the procedure described in the Experimental Methods after superposing 3GN4 utilizing overlapping Cα coordinates. Myosin, magenta, actin density map, grey. Nucleotides and ions are displayed in ball and stick representation and colored by heteroatom.
    Figure Legend Snippet: Morph between indicated states of the myosin VI mechanochemical cycle, aligned in the reference from of the actin filament. To generate this morph, the full ADP and rigor density maps were aligned, and then the LPF ADP MDFF and LPF rigor MDFF models were rigid body fit into their corresponding densities. The grafted lever arm models were then superimposed on the LPF MDFF models using overlapping Cα coordinates. For the Pre-Powerstroke (2V26) and PiR (4PFO) states, the X-ray structures were superimposed on the LPF ADP MDFF model based on the Cα coordinates of the full motor domain. For the post-rigor (2VAS) state, the x-ray structure was superimposed on the LPF rigor MDFF model based on the Cα coordinates of the full motor domain. The lever arms of crystal structures were extended in a manner analogous to the procedure described in the Experimental Methods after superposing 3GN4 utilizing overlapping Cα coordinates. Myosin, magenta, actin density map, grey. Nucleotides and ions are displayed in ball and stick representation and colored by heteroatom.

    Techniques Used:



    Similar Products

    dynamics flexible fitting (mdff) approach  (Molecular Dynamics Inc)
    90
    Molecular Dynamics Inc dynamics flexible fitting (mdff) approach
    Morph from the LPF ADP MDFF model to the LPF rigor MDFF model. To generate this morph, the ADP and rigor density maps were aligned, then their corresponding atomistic models were rigid body fit into the aligned maps. Myosin, magenta, three actin subunits, varying shades of blue.
    Dynamics Flexible Fitting (Mdff) Approach, 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+%28mdff%29+approach/pmc05762158-74-14-12?v=Molecular+Dynamics+Inc
    Average 90 stars, based on 1 article reviews
    dynamics flexible fitting (mdff) approach - by Bioz Stars, 2026-07
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    Morph from the LPF ADP MDFF model to the LPF rigor MDFF model. To generate this morph, the ADP and rigor density maps were aligned, then their corresponding atomistic models were rigid body fit into the aligned maps. Myosin, magenta, three actin subunits, varying shades of blue.

    Journal: eLife

    Article Title: Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity

    doi: 10.7554/eLife.31125

    Figure Lengend Snippet: Morph from the LPF ADP MDFF model to the LPF rigor MDFF model. To generate this morph, the ADP and rigor density maps were aligned, then their corresponding atomistic models were rigid body fit into the aligned maps. Myosin, magenta, three actin subunits, varying shades of blue.

    Article Snippet: Implementing novel adaptations of the Iterative Helical Real Space Reconstruction (IHRSR) and Molecular Dynamics Flexible Fitting (MDFF) approaches, we present a detailed model of the myosin VI-F-actin interface, and provide the first structure of myosin VI in the ADP state, to our knowledge the highest-resolution structure of any myosin in this state.

    Techniques:

    Morph from the ADP to rigor reconstruction, low-pass filtered at 7.5 Å focusing on the myosin VI nucleotide binding cleft with density corresponding to ADP nucleotide colored orange (left panel). To generate this morph, density maps aligned to each other. Right panel includes the LPF rigor MDFF model rigid body fit into the rigor density map.

    Journal: eLife

    Article Title: Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity

    doi: 10.7554/eLife.31125

    Figure Lengend Snippet: Morph from the ADP to rigor reconstruction, low-pass filtered at 7.5 Å focusing on the myosin VI nucleotide binding cleft with density corresponding to ADP nucleotide colored orange (left panel). To generate this morph, density maps aligned to each other. Right panel includes the LPF rigor MDFF model rigid body fit into the rigor density map.

    Article Snippet: Implementing novel adaptations of the Iterative Helical Real Space Reconstruction (IHRSR) and Molecular Dynamics Flexible Fitting (MDFF) approaches, we present a detailed model of the myosin VI-F-actin interface, and provide the first structure of myosin VI in the ADP state, to our knowledge the highest-resolution structure of any myosin in this state.

    Techniques:

    Morphs from actin alone to ADP, ADP to rigor, and rigor to actin alone focusing on the H-plug (red) and D-loop (orange). Right panels: Morphs of density maps, low-pass filtered to 7.5 Å and aligned to each other. Left panels: Morphs between backbone-averaged HR MDFF models. To generate the morphs of atomistic models, the density maps were aligned, then their corresponding atomistic models were rigid-body fit into the aligned maps.

    Journal: eLife

    Article Title: Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity

    doi: 10.7554/eLife.31125

    Figure Lengend Snippet: Morphs from actin alone to ADP, ADP to rigor, and rigor to actin alone focusing on the H-plug (red) and D-loop (orange). Right panels: Morphs of density maps, low-pass filtered to 7.5 Å and aligned to each other. Left panels: Morphs between backbone-averaged HR MDFF models. To generate the morphs of atomistic models, the density maps were aligned, then their corresponding atomistic models were rigid-body fit into the aligned maps.

    Article Snippet: Implementing novel adaptations of the Iterative Helical Real Space Reconstruction (IHRSR) and Molecular Dynamics Flexible Fitting (MDFF) approaches, we present a detailed model of the myosin VI-F-actin interface, and provide the first structure of myosin VI in the ADP state, to our knowledge the highest-resolution structure of any myosin in this state.

    Techniques:

    Morph between the backbone-averaged HR MDFF actin alone, ADP, and rigor models. Morphs generated as in <xref ref-type=Video 6 . " width="100%" height="100%">

    Journal: eLife

    Article Title: Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity

    doi: 10.7554/eLife.31125

    Figure Lengend Snippet: Morph between the backbone-averaged HR MDFF actin alone, ADP, and rigor models. Morphs generated as in Video 6 .

    Article Snippet: Implementing novel adaptations of the Iterative Helical Real Space Reconstruction (IHRSR) and Molecular Dynamics Flexible Fitting (MDFF) approaches, we present a detailed model of the myosin VI-F-actin interface, and provide the first structure of myosin VI in the ADP state, to our knowledge the highest-resolution structure of any myosin in this state.

    Techniques:

    Morph between indicated states of the myosin VI mechanochemical cycle, aligned in the reference from of the actin filament. To generate this morph, the full ADP and rigor density maps were aligned, and then the LPF ADP MDFF and LPF rigor MDFF models were rigid body fit into their corresponding densities. The grafted lever arm models were then superimposed on the LPF MDFF models using overlapping Cα coordinates. For the Pre-Powerstroke (2V26) and PiR (4PFO) states, the X-ray structures were superimposed on the LPF ADP MDFF model based on the Cα coordinates of the full motor domain. For the post-rigor (2VAS) state, the x-ray structure was superimposed on the LPF rigor MDFF model based on the Cα coordinates of the full motor domain. The lever arms of crystal structures were extended in a manner analogous to the procedure described in the Experimental Methods after superposing 3GN4 utilizing overlapping Cα coordinates. Myosin, magenta, actin density map, grey. Nucleotides and ions are displayed in ball and stick representation and colored by heteroatom.

    Journal: eLife

    Article Title: Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity

    doi: 10.7554/eLife.31125

    Figure Lengend Snippet: Morph between indicated states of the myosin VI mechanochemical cycle, aligned in the reference from of the actin filament. To generate this morph, the full ADP and rigor density maps were aligned, and then the LPF ADP MDFF and LPF rigor MDFF models were rigid body fit into their corresponding densities. The grafted lever arm models were then superimposed on the LPF MDFF models using overlapping Cα coordinates. For the Pre-Powerstroke (2V26) and PiR (4PFO) states, the X-ray structures were superimposed on the LPF ADP MDFF model based on the Cα coordinates of the full motor domain. For the post-rigor (2VAS) state, the x-ray structure was superimposed on the LPF rigor MDFF model based on the Cα coordinates of the full motor domain. The lever arms of crystal structures were extended in a manner analogous to the procedure described in the Experimental Methods after superposing 3GN4 utilizing overlapping Cα coordinates. Myosin, magenta, actin density map, grey. Nucleotides and ions are displayed in ball and stick representation and colored by heteroatom.

    Article Snippet: Implementing novel adaptations of the Iterative Helical Real Space Reconstruction (IHRSR) and Molecular Dynamics Flexible Fitting (MDFF) approaches, we present a detailed model of the myosin VI-F-actin interface, and provide the first structure of myosin VI in the ADP state, to our knowledge the highest-resolution structure of any myosin in this state.

    Techniques: