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At the MEME server page, there's a link to upload a customized background markov model (using the command line interface, this is the -bfile option). From there, there's a link to the MEME Man Page. Under "Objective Function", it specifies:
The background model is an n-order Markov model. By default, it is a 0-order model consisting of the ...
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What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?
If I understand what you're attempting to accomplish, as David said, this is a vigorous area of study in structural biology. I'll start by saying that a single amino acid substitution will often make virtually no difference in a structure, but there are proteins where a couple substitutions will convert an all alpha-helical protein to all beta-sheet, so I'll ...
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After you load the molecule in VMD, from the menu bar select Graphics->Representations... In the box labeled Selected Atoms, type "hetero" and hit enter. You should now see only your ligand (and whatever other non-protein/DNA atoms that happen to be in your PDB file). Hit the Create Rep button, enter "protein" in the Selected Atoms box and hit enter (you can ...
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