Is there a tool that finds a given amino-acid sequence in a given secondary structure?

Question

[homeo.morphizm]

Say, I want to find all proteins with a motif of "VAL TRP TYR" subject to a condition this motif has to populate an alpha-helix. Is there a bioinformatics tool for that?

[Mensur Dlakic]

Off the top of my head, no such tool has been reported, though someone has probably developed it. Part of the reason is that secondary structure is somewhat loosely defined, depending on the exact type of 8state -> 3state reduction.

It may help you to look at secondary structure propensities of all residues. I have calculated it about 10 years ago. For the tripeptide you asked about, an average helix propensity would be 0.964, which is middle of the road.

It was not much different from previously published numbers, and there may be a more recent (and published!) version available.