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

Julien Maupetit | Zendy; Romain Gautier | Zendy; Pierre Tufféry | Zendy

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

Author(s) -

Julien Maupetit,

Romain Gautier,

Pierre Tufféry

Publication year - 2006

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkl289

Subject(s) - trace (psycholinguistics) , biology , alphabet , alpha (finance) , line (geometry) , markov chain , carbon fibers , computational biology , algorithm , astrophysics , combinatorics , computer science , mathematics , physics , geometry , statistics , machine learning , philosophy , construct validity , linguistics , composite number , psychometrics

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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