What is Smiles2Monomers
Smiles2Monomers is a software to infer monomeric structure of polymers from their atomic structure.
On this webserver the software is dedicated to peptie-like compounds. To use the software on other kind of polymers, you can get the source code on GitHub under the GNU-AFFERO licence and pre-compute different kind of monomers.
The web server is available for peptide-like compounds in the second tab and provides an interface to upload a compound in the SMILES format to compute the monomeric structure in two different formats :
- Text formats : The structure is downloadable in json and xml
- Image format : The colored picture of the monomeric structure mapped on the atomic structure is directly available in the browser or downloadable into a zip file.
Tests
We tested s2m on two manually curated datasets: Norine and the Chemical Component Dictionary (at PDBe or at RCSB PDB). Among 341 nonribomosal peptides of Norine, s2m predicts correctly 253 polymers (see all the results). Among 378 polymers of CCD, s2m predicts correctly 322 polymers (see all the results).
Reference
Smiles2Monomers : a link between chemical and biological structures for polymers
Yoann Dufresne, Laurent Noé, Valérie Leclère and Maude Pupin
Journal of Cheminformatics, January 2016, doi:
10.1186/s13321-015-0111-5