KAKSI - secondary structure assignment:
KAKSI is a new secondary structure assignment method. This novel approach has been developped in Jean-Francois Gibrat's lab at
(INRA, Jouy-en-Josas, France) by Juliette Martin.
The secondary structure assignment, alpha helix (H), beta strands (b) and turns (T) is based on characteristic distances between alpha carbons and phi-psi angle values.
Coils (c) are the amino acids not associated to any of the different previous states.
This method pay a special attention to the detection of kinks in helices.
The geometry of helices is assessed using a dedicated software, HELANAL and the curvature of periodic secondary structures have been precisely analyzed.
Assignment made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR on 4 datasets
(X-ray structures with different resolution range, NMR structures).
As most of the secondary structure assignment method assign a high level of curved and kinked helices, KAKSI
has been designed to assign mainly linear helices (curvature of the backbone Calpha trace has also been analyzed).
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Some helices are simply a bit too long like the first exemple. | |
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Others, like the second exemple are clearly a wrong assignment. | |
KAKSI favors the assignment of several short helices when compared to STRIDE and PSEA.
KAKSI assigns slightly longer helices and strands than STRIDE.
Comparisons have been done with many other secondary structure assignments showing that KAKSI assign less curved or kinked helices that other methods.
We show that KAKSI provides some sort of consensus assignments, being equally distant from all other methods.
They are more linear than helices assigned by other methods. The same tendency, to split long segments, is observed, although less systematically, for strands.
KAKSI can be donwloaded at MIG : http://migale.jouy.inra.fr/?q=kaksi. Two versions can be found locally: first one (kaksi.tar) and latest (kaksi.tarball.tar). They gave similar results.
Reference:
Martin J., Letellier G., Marin A., Taly J.-F., de Brevern A.G. & Gibrat J.-F.(2005),
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods,
BMC Structural Biology, 5:17.
