Structural pattern matching of nonribosomal peptides
| Autor: | Phillipe Jacques, Valérie Leclère, Ségolène Caboche, Gregory Kucherov, Maude Pupin |
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| Přispěvatelé: | Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS), Sequential Learning (SEQUOIA), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire des Procédés Biologiques Génie Enzymatique et Microbien (PROBIOGEM), Université de Lille, Sciences et Technologies-Fédération Universitaire et Polytechnique de Lille |
| Jazyk: | angličtina |
| Rok vydání: | 2009 |
| Předmět: |
Protein Conformation
Computational biology Biology 01 natural sciences User-Computer Interface 03 medical and health sciences Protein structure Protein sequencing Structural Biology Nonribosomal peptide Peptide Biosynthesis Pattern matching Databases Protein Peptide structure lcsh:QH301-705.5 030304 developmental biology chemistry.chemical_classification graph comparison Internet 0303 health sciences 010405 organic chemistry Methodology Article Protein primary structure [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] 0104 chemical sciences Amino acid lcsh:Biology (General) chemistry Biochemistry Peptide Biosynthesis Nucleic Acid-Independent non-ribosomal peptides [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] Peptides |
| Zdroj: | BMC Structural Biology BMC Structural Biology, BioMed Central, 2009, 9 (15), ⟨10.1186/1472-6807-9-15⟩ BMC Structural Biology, 2009, 9 (15), ⟨10.1186/1472-6807-9-15⟩ BMC Structural Biology, Vol 9, Iss 1, p 15 (2009) |
| ISSN: | 1472-6807 |
| Popis: | Background Nonribosomal peptides (NRPs), bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents). NRPs are mainly composed of amino acids but their primary structure is not always linear and can contain cycles or branchings. Furthermore, there are several hundred different monomers that can be incorporated into NRPs. The NORINE database, the first resource entirely dedicated to NRPs, currently stores more than 700 NRPs annotated with their monomeric peptide structure encoded by undirected labeled graphs. This opens a way to a systematic analysis of structural patterns occurring in NRPs. Such studies can investigate the functional role of some monomeric chains, or analyse NRPs that have been computationally predicted from the synthetase protein sequence. A basic operation in such analyses is the search for a given structural pattern in the database. Results We developed an efficient method that allows for a quick search for a structural pattern in the NORINE database. The method identifies all peptides containing a pattern substructure of a given size. This amounts to solving a variant of the maximum common subgraph problem on pattern and peptide graphs, which is done by computing cliques in an appropriate compatibility graph. Conclusion The method has been incorporated into the NORINE database, available at http://bioinfo.lifl.fr/norine. Less than one second is needed to search for a pattern in the entire database. |
| Databáze: | OpenAIRE |
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