Smiles2Monomers: a link between chemical and biological structures for polymers

Yoann Dufresne 1, 2 Laurent Noé 1, 2 Valérie Leclère 3, 1, 2 Maude Pupin 1, 2
2 BONSAI - Bioinformatics and Sequence Analysis
Université de Lille, Sciences et Technologies, Inria Lille - Nord Europe, CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189, CNRS - Centre National de la Recherche Scientifique
Abstract : Background: The monomeric composition of polymers is powerful for structure comparison and synthetic biology , among others. Many databases give access to the atomic structure of compounds but the monomeric structure of polymers is often lacking. We have designed a smart algorithm, implemented in the tool Smiles2Monomers (s2m), to infer efficiently and accurately the monomeric structure of a polymer from its chemical structure. Results: Our strategy is divided into two steps: first, monomers are mapped on the atomic structure by an efficient subgraph-isomorphism algorithm ; second, the best tiling is computed so that non-overlapping monomers cover all the structure of the target polymer. The mapping is based on a Markovian index built by a dynamic programming algorithm. The index enables s2m to search quickly all the given monomers on a target polymer. After, a greedy algorithm combines the mapped monomers into a consistent monomeric structure. Finally, a local branch and cut algorithm refines the structure. We tested this method on two manually annotated databases of polymers and reconstructed the structures de novo with a sensitivity over 90 %. The average computation time per polymer is 2 s. Conclusion: s2m automatically creates de novo monomeric annotations for polymers, efficiently in terms of time computation and sensitivity. s2m allowed us to detect annotation errors in the tested databases and to easily find the accurate structures. So, s2m could be integrated into the curation process of databases of small compounds to verify the current entries and accelerate the annotation of new polymers. The full method can be downloaded or accessed via a website for peptide-like polymers at
Type de document :
Article dans une revue
Journal of Cheminformatics, Chemistry Central Ltd. and BioMed Central, 2015, 〈10.1186/s13321-015-0111-5〉
Liste complète des métadonnées

Littérature citée [35 références]  Voir  Masquer  Télécharger
Contributeur : Maude Pupin <>
Soumis le : mardi 5 janvier 2016 - 09:45:26
Dernière modification le : vendredi 22 mars 2019 - 01:34:52
Document(s) archivé(s) le : jeudi 7 avril 2016 - 14:59:47


Fichiers éditeurs autorisés sur une archive ouverte



Yoann Dufresne, Laurent Noé, Valérie Leclère, Maude Pupin. Smiles2Monomers: a link between chemical and biological structures for polymers. Journal of Cheminformatics, Chemistry Central Ltd. and BioMed Central, 2015, 〈10.1186/s13321-015-0111-5〉. 〈hal-01250619〉



Consultations de la notice


Téléchargements de fichiers