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Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W147-51.

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

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  • 1Equipe de Bioinformatique Génomique et Moléculaire, INSERM U726, Université Paris 7, case 7113, 2, place Jussieu, 75251 Paris cedex 05, France.

Abstract

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.

PMID:
16844979
PMCID:
PMC1538914
DOI:
10.1093/nar/gkl289
[PubMed - indexed for MEDLINE]
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