Is there a tool that finds a given amino-acid sequence in a given secondary structure?
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?
• 884 views
•
link
updated
by
Ram
•
written
by
homeo.morphizm •
•
written
by
homeo.morphizm •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
bulk mapping of aa residue to protein structural features
written by wildtype •
-
Help translating RNA to amino acid sequence
written by biocoding4444 •
-
Editing angles of PDB files
written by michael •
-
Command line tool for Helix-Turn-Helix motif predictions
written by hed.robin •
-
Is there any database to find the protein interfaces that already found experimentally?
written by m.koohi.m
-
Find out motif
written by Zaved Hazarika •
-
Searching for conserved short motifs
written by Saulius Lukauskas
-
Determine Which Atoms Are Part Of The Alpha Helix
written by GreenDiamond
-
Database For Motifs Or Motif Scanning Tools Or Functional Prediction.
written by Wayne
-
Finding Single Domain Proteins
written by Fernando •
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 -> 3statereduction.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.