ZIOC launched a database of carbohydrates conformations

The ability to obtain data on the three-dimensional structure of carbohydrates derivatives is in demand in glycochemistry and glycobiology. The work of scientists in these areas has often been hampered by the lack of user tools that do not require the researcher to understand the informatics aspects of computational chemistry. Such a tool is being developed as part of the development of the Carbohydrate Structure Database platform (http://csdb.glycoscience.ru) by the researchers of the Academician N.K. Kochetkov Laboratory of Carbohydrates and Biocides of the ZIOC. A critical step for the automatic assembly of more complex structures is to provide fast access to the conformational data of small structural fragments. So, in 2021, a service for predicting the predominant conformations of oligosaccharides appeared. It uses a database of 100ns molecular dynamics trajectories pre-calculated in the MM3 field with sheer water. According to the results of previous studies of the nuclear Overhauser effect of carbohydrates, this method of simulating their molecular geometry gives an accuracy comparable to quantum mechanical calculations, while surpassing the latter in performance by two orders. The database is web-based and structure searchable and provides interactive conformational maps of several thousand of disaccharides. It is also regularly updated with data calculated on the computing server of the Academician N.K. Kochetkov Laboratory of Carbohydrates and Biocides in automatic mode.

Source:

Sofya I. Scherbinina, Martin Frank, Philip V. Toukach Carbohydrate Structure Database (CSDB) oligosaccharide conformation tool – Glycobiology 2022, cwac011. DOI: 10.1093/glycob/cwac011