24 July 2001

Release 1.1 substitutes release 1.0_new. This release has improvements to speed up the search in the most recent release of dbs.

Starting from today, the News page will inform about modifications to the web pages.

HELM is a software developed to search for HELix Motifs within protein sequences. Please quote it by the following reference:

A.M. Facchiano (2000) HELM: searching for helix motifs within protein sequences. Bioinformatics, 16, 292-293.

A brief description:

HELM is a web interface to find helix motifs within protein sequences. Over the years, a lot of papers have been published about helix motifs. HELM was originally wrote to find stabilising factors within helices, and it was continuously updated in order to find new described motifs.
Recently, helix motifs have been reviewed by Aurora and Rose ("Helix capping", Protein Science, 1998, 7, 21-38) and HELM has been updated to find the motifs described by Aurora and Rose.

Definition of residue position

The position of residues in (and out of) the helix are defined according this nomenclature:

N4'-N'''-N''-N'-Ncap(the first residue of the helix)-N1-N2-N3- ... -C3-C2-C1-Ccap(the last residue of the helix)-C'-C''-C'''-C4'

Definition of residue classes

Helix motifs consist of sequences in which specific classes of residues are found at specific positions. The classes used in the motif description are:
h = hydrophobic residues (Ala, Val, Ile, Leu, Met, Phe, Trp, Cys, neutral His and the alkyl side-chain moieties of Arg and Lys);
p = polar (Gly, Ser, Thr, Asn, Gln, Asp, Glu, Lys, Arg and protonated His);
n = non-beta branched = not (Val,Ile, Thr, Pro);
x = indifferent

Helix motifs

Here is the list of motifs describer by Aurora and Rose:

N-terminal motifs
Ia = h-xpxhx
Ib = h-xpxph
IIa = hp-xpxhx
IIb = hp-xpxph
IIIa = hpp-xpxhx
IIIb = hpp-xpxph

C-terminal motifs
IV = hxph-Gh
Va = hxpx-nxh
Vb = hxpx-nxph
VIa = hxxx-Gpxh
VIb = hxxx-Gpxph
VIIa = hxxx-Ppxh
VIIb = hxxx-Ppxph

The hyphen symbol (-) indicates the start of the helix (or the end, for C-terminal motifs).

As an example of explanation for the notation, Motif Ia starts at the N' residue with an hydrophobic residue, a polar residue is at the N1 position and an hydrophobic residue is at N3 position. Ncap and N2 positions can be occupied by any residue.

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