SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace.
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.
Maupetit
Julien
J
Equipe de Bioinformatique Génomique et Moléculaire, INSERM U726, Université Paris 7, case 7113, 2, place Jussieu, 75251 Paris cedex 05, France.
Gautier
R
R
Tufféry
Pierre
P
D002244:Carbon / Q000737:chemistry; D020407:Internet; D008390:Markov Chains; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D012984:Software
D010455:Peptides; D002244:Carbon