The function similarity between two protein sequences is quantified by relating the term specificities of the two terms and the specificity of their common ancestor term. Using this function similarity metric, the relationship between sequence similarity and function similarity can be modeled.
To demonstrate the similarities and differences between two protein sequences, they can be compared. In order to reduce the Root Mean Square (RMS) discrepancy between the second protein and the first geometry, the second of the two proteins is rotated and translated. If switching out atom pairs would lower the RMS error, it is done. There are three ways to depict differences. The most straightforward is to create a list of the atoms whose positions differ by the most, however this is only partially useful because some protein components are very flexible, meaning that huge geometric changes may be followed by only very tiny changes in energy. Changes in bond lengths are a more significant form of variation. Considering the high force constants of covalent bonds, any substantial change in bond length.
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