REStLESS: automated translation of glycan sequences from residue-based notation to SMILES and atomic coordinates

• Published in: Bioinformatics Vol. 34; no. 15; pp. 2679 - 2681
• Main Authors: Chernyshov, Ivan Yu, Toukach, Philip V
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.08.2018
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bty168

Abstract Motivation Glycans and glycoconjugates are usually recorded in dedicated databases in residue-based notations. Only a few of them can be converted into chemical (atom-based) formats highly demanded in conformational and biochemical studies. In this work, we present a tool for translation from a residue-based glycan notation to SMILES. Results The REStLESS algorithm for translation from the CSDB Linear notation to SMILES was developed. REStLESS stands for ResiduEs as Smiles and LinkagEs as SmartS, where SMARTS reaction expressions are used to merge pre-encoded residues into a molecule. The implementation supports virtually all structural features reported in natural carbohydrates and glycoconjugates. The translator is equipped with a mechanism for conversion of SMILES strings into optimized atomic coordinates which can be used as starting geometries for various computational tasks. Availability and implementation REStLESS is integrated in the Carbohydrate Structure Database (CSDB) and is freely available on the web (http://csdb.glycoscience.ru/csdb2atoms.html). Supplementary information Supplementary data are available at Bioinformatics online.