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The structure activity relationship is less well defined, as no distinct binding pockets are present.
Similar(59)
Only a single methyl-lysine-binding pocket is present in all MBT-repeat proteins, whereas the corresponding 'pockets' in the other repeats are shallower and less well conserved.
Sequence alignments using the identified β-valinyl CoA ligase, PaaK1 and PaaK2 demonstrated that the ATP-binding pocket is present in the identified β-valinyl CoA ligase.
Binding pockets are correctly predicted in 94% and 93% of the datasets.
The binding pockets are fairly large.
Four binding pockets are marked as A, B, C, and D. Another binding pocket is marked as LBD.
The five highly conserved crystal waters present in all BET bromodomains binding pockets were kept, whereas all other waters and organic molecules were removed.
Efficient determination of structural similarities between protein binding pockets is an important challenge in computational chemistry.
Determination of similarities between protein binding pockets is an important challenge in computer-aided drug design.
This is supported by two points: (i) the experimental approach developed here is biologically relevant since the binding of bisphenol A (BPA) to amphiER was observed using the same experimental conditions as for E2 suggesting that amphiER is correctly folded and that a ligand binding pocket is likely to be present.
Occasionally, major monovalent cation-binding pockets are detected by simulations.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com