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Nucleic Acids Research 2006 34(Web Server issue):W147-W151; doi:10.1093/nar/gkl289
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace

Julien Maupetit, R. Gautier1 and Pierre Tufféry*

Equipe de Bioinformatique Génomique et Moléculaire, INSERM U726, Université Paris 7 case 7113, 2, place Jussieu, 75251 Paris cedex 05, France 1 Institut de Pharmacologie Moléculaire et Cellulaire, UMR 6097 CNRS/UNSA 660 route des Lucioles, 06560 Sophia Antipolis, France

*To whom correspondence should be addressed. Tel: 331 44 27 77 33; Fax: 331 43 26 38 30; Email: tuffery{at}ebgm.jussieu.fr

Received February 10, 2006. Revised March 2, 2006. Accepted April 5, 2006.

SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments taken from a library of reduced size, selected from the encoding of the protein trace in a hidden Markov model-derived structural alphabet. The assembly of the fragments is achieved by a greedy algorithm, using an energy-based scoring. Alpha-carbon coordinates remain unaffected. SABBAC simply positions the missing backbone atoms, no further refinement is performed. From our tests, SABBAC performs equal or better than other similar on-line approach and is robust to deviations on the alpha-carbon coordinates. It can be accessed at http://bioserv.rpbs.jussieu.fr/SABBAC.html.


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