Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Abstract

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.