Jbo. Mitchell, The relationship between the sequence identities of alpha helical proteinsin the PDB and the molecular similarities of their ligands, J CHEM INF, 41(6), 2001, pp. 1617-1622
Citations number
18
Categorie Soggetti
Chemistry
Journal title
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
This paper considers the relationship between the percentage sequence ident
ities of protein chains and the molecular similarities of the ligands they
bind. Among a set of alpha helical proteins from the PDB, it is found that
related proteins tend to bind similar ligands. Furthermore, the property of
binding similar ligands can be used to define the categories of "like" and
"unlike" pairs of protein chains, separated by an approximate cutoff at a
sequence identity of, or somewhat above, 45%. Similarly, the property of bi
nding related protein chains can be used to define "low" and "high" similar
ity pairs of ligand residues, with a cutoff at a Tanimoto score of 0.70. Th
e ligands bound to two "like" protein chains are five times more likely to
be of high similarity than would be expected if protein sequence identity a
nd ligand molecular similarity were independent variables. Nonetheless, the
nature of the PDB means that it is unclear whether the same conclusions wo
uld be reached with a data set representing an unbiased sample of all prote
in-ligand complexes in a living cell. The construction of an appropriate da
ta set for such a study represents a significant challenge.