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.

Motivation: Carbohydrates play crucial roles in various biochemical processes and are useful for developing drugs and vaccines. However, in case of carbohydrates, the primary structure elucidation is usually a sophisticated task. Therefore, they remain the least structurally characterized class of biomolecules, and it hampers the progress in glycochemistry and glycobiology. Creating a usable instrument designed to assist researchers in natural carbohydrate structure determination would advance glycochemistry in biomedical and pharmaceutical applications. Results: We present GRASS (Generation, Ranking and Assignment of Saccharide Structures), a novel method for semi-automated elucidation of carbohydrate and derivative structures which uses unassigned 13C NMR spectra and information obtained from chromatography, optical, chemical and other methods. This approach is based on new methods of carbohydrate NMR simulation recently reported as the most accurate. It combines a broad diversity of supported structural features, high accuracy and performance. Availability and implementation: GRASS is implemented in a free web tool available at http://csdb.glycoscience.ru/grass.html. Contact: [email protected] or [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.

MOTIVATION: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. RESULTS: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. AVAILABILITY AND IMPLEMENTATION: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/).