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namd program with the molecular dynamics flexible fitting (mdff) protocol  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc namd program with the molecular dynamics flexible fitting (mdff) protocol
    Namd Program With The Molecular Dynamics Flexible Fitting (Mdff) Protocol, 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+protocol/mdff++molecular+dynamics+flexible+fitting+/pmc08230804-272-1-5
    Average 90 stars, based on 1 article reviews
    namd program with the molecular dynamics flexible fitting (mdff) protocol - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Comparison:

    Article Title: Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1
    Article Snippet: small ribosomal subunit; that feature can snugly accommodate the 99-aa domain III, and is therefore tentatively assigned to domain III of IF2 mt . .. The final atomic model of IF2 mt was obtained by flexible fitting into the cryo-EM density corresponding to IF2 mt ( ) using the Molecular Dynamics Flexible Fitting (MDFF) protocol ( 34 ). .. An atomic structure of the tRNA (PDB code 1ZO3) ( 12 ) was fit into the densities that correspond to the initiator and E-site tRNAs.

    Cryo-EM Sample Prep:

    Article Title: Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1
    Article Snippet: small ribosomal subunit; that feature can snugly accommodate the 99-aa domain III, and is therefore tentatively assigned to domain III of IF2 mt . .. The final atomic model of IF2 mt was obtained by flexible fitting into the cryo-EM density corresponding to IF2 mt ( ) using the Molecular Dynamics Flexible Fitting (MDFF) protocol ( 34 ). .. An atomic structure of the tRNA (PDB code 1ZO3) ( 12 ) was fit into the densities that correspond to the initiator and E-site tRNAs.

    Sequencing:

    Article Title: Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1
    Article Snippet: small ribosomal subunit; that feature can snugly accommodate the 99-aa domain III, and is therefore tentatively assigned to domain III of IF2 mt . .. The final atomic model of IF2 mt was obtained by flexible fitting into the cryo-EM density corresponding to IF2 mt ( ) using the Molecular Dynamics Flexible Fitting (MDFF) protocol ( 34 ). .. An atomic structure of the tRNA (PDB code 1ZO3) ( 12 ) was fit into the densities that correspond to the initiator and E-site tRNAs.

    Residue:

    Article Title: Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1
    Article Snippet: small ribosomal subunit; that feature can snugly accommodate the 99-aa domain III, and is therefore tentatively assigned to domain III of IF2 mt . .. The final atomic model of IF2 mt was obtained by flexible fitting into the cryo-EM density corresponding to IF2 mt ( ) using the Molecular Dynamics Flexible Fitting (MDFF) protocol ( 34 ). .. An atomic structure of the tRNA (PDB code 1ZO3) ( 12 ) was fit into the densities that correspond to the initiator and E-site tRNAs.

    Binding Assay:

    Article Title: Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1
    Article Snippet: small ribosomal subunit; that feature can snugly accommodate the 99-aa domain III, and is therefore tentatively assigned to domain III of IF2 mt . .. The final atomic model of IF2 mt was obtained by flexible fitting into the cryo-EM density corresponding to IF2 mt ( ) using the Molecular Dynamics Flexible Fitting (MDFF) protocol ( 34 ). .. An atomic structure of the tRNA (PDB code 1ZO3) ( 12 ) was fit into the densities that correspond to the initiator and E-site tRNAs.

    Centrifugation:

    Article Title: Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1
    Article Snippet: small ribosomal subunit; that feature can snugly accommodate the 99-aa domain III, and is therefore tentatively assigned to domain III of IF2 mt . .. The final atomic model of IF2 mt was obtained by flexible fitting into the cryo-EM density corresponding to IF2 mt ( ) using the Molecular Dynamics Flexible Fitting (MDFF) protocol ( 34 ). .. An atomic structure of the tRNA (PDB code 1ZO3) ( 12 ) was fit into the densities that correspond to the initiator and E-site tRNAs.

    SDS Page:

    Article Title: Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1
    Article Snippet: small ribosomal subunit; that feature can snugly accommodate the 99-aa domain III, and is therefore tentatively assigned to domain III of IF2 mt . .. The final atomic model of IF2 mt was obtained by flexible fitting into the cryo-EM density corresponding to IF2 mt ( ) using the Molecular Dynamics Flexible Fitting (MDFF) protocol ( 34 ). .. An atomic structure of the tRNA (PDB code 1ZO3) ( 12 ) was fit into the densities that correspond to the initiator and E-site tRNAs.



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    dynamics flexible fitting protocol  (Molecular Dynamics Inc)
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    Comparison of the domain organization of E. coli <t>IF2</t> and mammalian IF2mt, and cryo-EM structure of the complex. (A) Domain alignment of E. coli IF2 and bovine IF2mt. Note that the mature IF2mt (i.e., after deletion of the import sequence) starts from aa residue 78. The 37-aa insertion in IF2mt is highlighted in red. (B) The cryo-EM map of the E. coli 70S ribosome (30S subunit, yellow; 50S subunit, blue) in complex with IF2mt (red), initiator tRNA (green) at the P/I position, and an additional tRNA density (brown, visible in panels C and D) at the ribosomal E site. (C and D) The 30S and 50S subunit portions of the map are shown from their interface sides to reveal the overall binding positions of IF2mt and tRNAs. Landmarks of the 30S subunit: h, head; sh, shoulder; b, body; and pt, platform. Landmarks of the 50S subunit: L1, L1 protein protuberance; CP, central protuberance; and Sb, L7/L12 stalk base. For stereo viewing, see Fig. S2.
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    Image Search Results


    Comparison of the domain organization of E. coli IF2 and mammalian IF2mt, and cryo-EM structure of the complex. (A) Domain alignment of E. coli IF2 and bovine IF2mt. Note that the mature IF2mt (i.e., after deletion of the import sequence) starts from aa residue 78. The 37-aa insertion in IF2mt is highlighted in red. (B) The cryo-EM map of the E. coli 70S ribosome (30S subunit, yellow; 50S subunit, blue) in complex with IF2mt (red), initiator tRNA (green) at the P/I position, and an additional tRNA density (brown, visible in panels C and D) at the ribosomal E site. (C and D) The 30S and 50S subunit portions of the map are shown from their interface sides to reveal the overall binding positions of IF2mt and tRNAs. Landmarks of the 30S subunit: h, head; sh, shoulder; b, body; and pt, platform. Landmarks of the 50S subunit: L1, L1 protein protuberance; CP, central protuberance; and Sb, L7/L12 stalk base. For stereo viewing, see Fig. S2.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1

    doi: 10.1073/pnas.1017425108

    Figure Lengend Snippet: Comparison of the domain organization of E. coli IF2 and mammalian IF2mt, and cryo-EM structure of the complex. (A) Domain alignment of E. coli IF2 and bovine IF2mt. Note that the mature IF2mt (i.e., after deletion of the import sequence) starts from aa residue 78. The 37-aa insertion in IF2mt is highlighted in red. (B) The cryo-EM map of the E. coli 70S ribosome (30S subunit, yellow; 50S subunit, blue) in complex with IF2mt (red), initiator tRNA (green) at the P/I position, and an additional tRNA density (brown, visible in panels C and D) at the ribosomal E site. (C and D) The 30S and 50S subunit portions of the map are shown from their interface sides to reveal the overall binding positions of IF2mt and tRNAs. Landmarks of the 30S subunit: h, head; sh, shoulder; b, body; and pt, platform. Landmarks of the 50S subunit: L1, L1 protein protuberance; CP, central protuberance; and Sb, L7/L12 stalk base. For stereo viewing, see Fig. S2.

    Article Snippet: The final atomic model of IF2 mt was obtained by flexible fitting into the cryo-EM density corresponding to IF2 mt ( ) using the Molecular Dynamics Flexible Fitting (MDFF) protocol ( 34 ).

    Techniques: Comparison, Cryo-EM Sample Prep, Sequencing, Residue, Binding Assay