Enhancements to the AllAll server at ETHZ
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A preliminary version of the SIAPrediction (Surface-Inside-Active
site) routine has been added to the all-against-all e-mail server at
ETHZ.
If SIAPrediction is requested, each position of a multiple protein
alignment is assigned as being either on the surface ('S' or 's') or
the interior ('I' or 'i') under the assumption that all members of the
multiple alignment have the same tertiary structure.
The prediction of surface and interior positions from a multiple
alignment is the basis of the ETH method for predicting the secondary
structure of a protein family [1]. The surface and interior assignments can
be used for the prediction of coil regions, helices and strands. A
region in a multiple alignment which shows alternating periodicity
(e.g. ISISISI) can be assigned as an amphiphilic beta strand. A region
which shows 3.6 periodicity (e.g. SIISSISSIIS) can be assigned as an
amphiphilic alpha helix. A region which contains mainly surface
assignments can be assigned as a coil and regions which contain mainly
interior assignments can be assigned as internal strands or helices.
For a complete example see [2].
For more information, send the message "Help" or "Help AllAll" to
cbrg at inf.ethz.ch
References:
[1] S.A. Benner, I. Badcoe, M.A. Cohen, D.L. Gerloff: Bona Fide
Prediction of Aspects of Protein Conformation: Assigning
Interior and Surface Residues from Patterns of Variation
and Conservation in Homologous Protein Sequences.
J. Mol. Biol. (1993) in press.
[2] D.L. Gerloff, T.F. Jenny, L.J. Knecht, S.A. Benner: A Secondary
Structure Prediction of the Hemorrhagic Metalloprotease Family.
Biochem. Biophys. Res. Commun., 194 (1993) 560-565.
