REStLESS：基于残基表示的聚糖序列到 SMILES 和原子坐标的自动翻译。

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

机构信息

All-Russia Research Institute of Agricultural Biotechnology, Laboratory of Plant Stress Tolerance, Russian Academy of Sciences, Moscow, Russia.

Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Laboratory of Complex and Nano-scaled Catalysts, Moscow, Russia.

出版信息

Bioinformatics. 2018 Aug 1;34(15):2679-2681. doi: 10.1093/bioinformatics/bty168.

DOI:10.1093/bioinformatics/bty168

PMID:29547883

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.

摘要

动机

聚糖和糖缀合物通常以基于残基的符号记录在专用数据库中。只有其中的少数可以转换为构象和生化研究中高度需要的化学（基于原子）格式。在这项工作中，我们提出了一种从基于残基的聚糖符号到 SMILES 的翻译工具。

结果

开发了用于将 CSDB Linear 符号转换为 SMILES 的 REStLESS 算法。REStLESS 代表残基作为 SMILES 和键作为 SmartS，其中使用 SMARTS 反应表达式将预编码的残基合并到一个分子中。该实现支持天然碳水化合物和糖缀合物中报告的几乎所有结构特征。该翻译器配备了一种将 SMILES 字符串转换为可优化原子坐标的机制，这些坐标可用于各种计算任务的起始几何形状。