Substitution Matrices

Protein structure and function are surprisingly resistant to polypeptide substitution, to the degree that the substitutions don't alter the chemistry of the protein. Substitutions are common over large expanses of time and from one species to the next. In many cases, the substitution of polypeptides through evolution can be predicted. In this way, a matrix of likely polypeptide substitutions can be constructed. As in a dot matrix analysis, the amino acids are listed across the top and side of a matrix, typically using the amino acid code letters listed in Table 8-3. At each intersection, the matrix is filled with a score that reflects how often one polypeptide would have been paired with the other in an alignment of related ...

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