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By 1961 Crick had evidence to show that each group of three bases (a codon) on a single DNA strand designates the position of a specific amino acid on the backbone of a protein molecule.
Catalytic cleavage of the backbone of a protein related to a disease may cure the disease.
Then, side-chain cover sets are used to optimize the conformation of the side chains given the coordinates of the backbone of a protein.
Because the polypeptide backbone of a protein is a linked sequence of rigid planar peptide groups, these two angles essentially determine the backbone conformation of proteins.
A refining procedure is then applied to identify its precise location through the following steps, Starting from the initially assigned opening point (o) and moving a probe (p) along the backbone of a protein (Q), two directions are applied including towards the peak (the well-superimposed region) and towards the bifurcation of the structural superposition.
The secondary structure constitutes the backbone of a protein which is essentially made of highly regular substructures of α-helices and β-strands.
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Faraggi et al. (2009) first predict the backbone angles of a protein using a machine learning method and then explore protein conformation search space using a genetic algorithm, based upon the predicted backbone angles.
This is the first-ever report of a crystal structure of the backbone of a circularized protein.
As is evident in Figure 3(a), the backbone of the protein acquired stability after 8 ns with a root mean square deviation (RMSD) of only about 2.5 Å from its initial position.
A cleavable linker that can replace an amino acid residue in the backbone of a (poly)peptide or protein will allow cleavage of the backbone into at least two fragments upon application of a defined trigger, but will require accessibility of the cleavage site to the trigger.
The residues have defined attachment points, allowing automated traversal of a protein backbone, or location of non-backbone bonds to residues.
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