SA-Search: a web tool for protein structure mining based on a Structural Alphabet.
SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.
Guyon
Frédéric
F
Equipe de Bioinformatique Génomique et Moléculaire, INSERM E346, Université Paris 7, Case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France. guyon@ebgm.jussieu.fr
Camproux
Anne-Claude
AC
Hochez
Joëlle
J
Tufféry
Pierre
P
D000595:Amino Acid Sequence; D020407:Internet; D008390:Markov Chains; D011487:Protein Conformation; D016415:Sequence Alignment; D012984:Software; D040681:Structural Homology, Protein