The key idea behind deducing function from structure
is that protein structure is better conserved than
sequence, and structure therefore provides a way of
homology database searching that is more sensitive
than sequence comparison.Hence, the logical first step
in analysing a newly solved structural genomics protein
is a structure comparison with the Protein Data Bank
(PDB)74, a database of known structures, using any of
various popular tools55,75–78.However, none of these
methods is guaranteed to find true matches in the database,
and any of them can report high scores for evolutionarily
unrelated proteins. Moreover, structural
similarity alone is insufficient to determine whether
two proteins are homologous, because they could have
evolved by convergence to have the same structure.