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HELM - Examples and tests
Example 1: Analysis of a simple protein
The 3D structure of the crambin (PDB and NRL3D code: 1crn) reveals the
presence of two helical segments, i.e. 7-19 and 23-30. HELM results evidence
the presence of helix motifs in these regions.
Example 2: Analysis of an all-beta protein
Barwin is a wound-induced protein from barley, classified as a all-beta
structure (very short helices can be recognized but they do not represent
a real structural feature). The sequence contains different helix motifs,
that evidently do not correspond to helix segments.
Example 3: Analysis of a membrane protein
The vasoactive intestinal polypeptide receptor 1 (SWISSPROT code: P32241)
is a membrane protein with seven transmembrane helices. The helix segments
reported in the SwissProt entry correspond to different helix motifs found
by HELM. It must be considered that no membrane protein was present in
the data set used by Aurora and Rose to extract their helix motif
classification, therefore, these motifs can be considered not specific for
The ability of HELM to find correctly the helix motifs has been verified
by visual inspection of sequences. Moreover, the accuracy of HELM has
been tested by analyzing a set of 1106 protein sequences derived from
the pdb_select data set (May 1999 release) and comparing
results to the analysis published by Aurora and Rose (1998). These
Authors analyzed a similar data set consisting of 274 protein sequences
(pdb_select, March 1994 release) and reported the number
of occurrence for each helix motif within the protein data set. Differences
between these two data sets consist mainly in the number of protein sequences
but both should represent a unique set of proteins, without significant
sequence identity. A higher occurrence of helix motifs can be expected
in the HELM test, because a higher number of protein has been analyzed.
Therefore, the occurrence of each motif has been compared between the two
data set by calculating the correlation coefficient, which resulted 0.837
and demonstrates a good agreement between the HELM test and the
previous analysis by Aurora and Rose.
Click here to see the results of the
HELM analysis. For each protein contained in the pdb_select data set
(May 1999 release) it is reported the occurrence of each motif.