GLYCAM Bacterial Carbohydrate Builder: a web-tool for modelling 3D structures of bacterial glycans

Abstract

Here we present the GLYCAM Bacterial Carbohydrate Builder (https://glycam.org/cb), an enhanced version of the GLYCAM-Web Carbohydrate Builder1 structure modeller that integrates support for modelling bacterial glycans, enabling the straightforward generation of three-dimensional structural models. The tool integrates bacterial monosaccharide parametrisations into a curated, user-friendly web-based resource. It provides an intuitive interface for the generation of carbohydrate sequences and generates 3D structural models in PDB file format, as well as the input files required for performing molecular dynamics simulations with the AMBER software package. The current implementation includes a library of 18 bacterial monosaccharides, which can be used in combination with the already parametrised eukaryotic sugars to construct complex bacterial glycans. Common derivatives, including acetylation, methylation, and sulfation are also supported. By validating and integrating bacterial sugar parameters into the GLYCAM-Web Carbohydrate Builder, this work reduces the technical barriers associated with bacterial glycan modelling and facilitates computational studies of complex bacterial glycoconjugates.