The program Alerting of Structurally Ambivalent
Sequences (ASAS) parses the submitted sequence, matching its
subsequences (tetrapeptides to nonapeptides) against our dataset of peptides
which are structural ambivalent between alpha-helix and beta-strand. Due
to the high structural flexibility of short peptides, we only list strongly
structurally ambivalent tetrapeptides and pentapeptides. A peptide is defined
to be strongly structurally ambivalent if it has been found in n
pairs of proteins in the representative protein database (with sequence
identity threshold 25%, Hobohm and Sander, version May 1999) of which m
pairs show helix-to-strand transition, where m>=2
and m/n>0.5. Longer subsequences
(hexa- to nonapeptides) are returned if they have shown any structural
ambivalence in the representative protein database with sequence identity
threshold 25% and 95%. For hexa- to nonapeptides, information about the
names of the constituent protein pairs, as well as the local secondary
structures of the structurally ambivalent peptides, are made available
for the user.
Submit and view results online (see also the example):
Reference: X.Zhou, F.Alber, G.Folkers,
G.Gonnet and G.Chelvanayagam. An analysis of the helix-to-strand transition
between peptides with identical sequence. Proteins 2000. In press
