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DetailsWe finally pick 1bdm:A over 1b8p:A and 7mdh:A because of its better crystallographic R-factor (16.9%) and higher overall sequence identity to the query sequence (45%). 3. Aligning TvLDF with the template. A good way of aligning the sequence of TvLDH with the structure of 1bdm:A is the align2d () command in MODELLER.
DetailsOptimization of the objective function by M. Equations used in the derivation of the molecular pdf. Rigid bodies. scripts from old M. commands and variables. models and alignments. to Python correspondence. MODELLER A Program for Protein Structure Modeling Release 10.4, r12463.
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DetailsThe size of the latest installation package available for download is 10.1 . Our built-in antivirus scanned this download and rated it as safe. The actual developer of the software is Andrej Sali Lab, UCSF. The most frequent installer filenames for the program include: cmd.exe, mdm.exe, Modeller.exe and modeller9.16-32bit.exe etc.
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DetailsTutorial. Advanced example: Modeling of a protein-ligand complex based on multiple templates, loop refinement and user specified restraints. All input and output files for this example are available to download, in either zip format (for Windows) or .tar.gz format (for Unix/Linux). For this example we will not describe step-by-step all MODELLER ...
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