ABSTRACT
Alignment: correspondence between the amino acids of two or more proteins Homology modeling: technique for the prediction of the three-dimensional
structure of a protein that relies on the possibility of using the structure of a homologous protein as starting model
Loop: region with nonrepetitive structure (i.e., not alpha or beta) Rotamer library: list of the most frequently observed dihedral angles for each
amino acid side chain Sequence identity: percentage of identical amino acids between two aligned
sequences Sequence similarity: score of an alignment obtained by adding the similarity
values for each pair of aligned amino acids. The similarity value of a pair of amino acids can be derived taking into account their chemical and physical similarity, the frequency with which they replace each other during evolution, or the minimal number of DNA base replacements needed to change the codon codifying for one in a codon codifying for the other.
