Mt. Semertzidis et al., HYDROPHOBIC NEIGHBORING HOMOLOGY (HNH) DOTPLOT - AN APPROACH FOR ASSESSING STRUCTURALLY SIMILAR MOTIFS IN PROTEINS, Computer methods and programs in biomedicine, 45(4), 1994, pp. 265-282
Structural biology needs sensitive tools to detect homology between pr
oteins of low sequence identity, but with closely related 3-D structur
es. Using a conventional dotplot method, we therefore introduced 2 con
cepts to improve the search for similarities between secondary structu
res of analyzed proteins: 'hydrophobic neighboring homology' (HNH) and
'amino acid degeneracy classes'. The amino acids are grouped into 3 s
ubsets: hydrophobic, hydrophilic and mimetic, A 'Neighboring Similarit
y Index' (NSI) is calculated for every residue pair and quantifies its
neighbor homology. By thresholding the homology matrix and filtering
the dotplot, the homologous patterns are extracted. We have evaluated
the efficiency and limits of the method using 21 protein pairs extract
ed from the Protein Data Bank (PDB), or selected from the recent liter
ature. Globally, we again find the homologous structures (alpha-helice
s and beta-strands) of these pair proteins, The introduction of neighb
or residue hydrophobicity in the conventional dotplot improves the ali
gnment of proteins with low sequence identity (< 25%). HNH, written in
standard ANSI C with the graphic library X11, under UNIX, is availabl
e on request.