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

Wan, Zhangmin; Yu, Yan; Bautista, Gio Ferson M.; Srebnik, Simcha; Smith, Jeremy C.; Rojas, Orlando J.

doi:10.1021/acs.jcim.5c01204

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

Journal Article · Thu Sep 04 00:00:00 EDT 2025 · Journal of Chemical Information and Modeling

DOI:https://doi.org/10.1021/acs.jcim.5c01204· OSTI ID:3002389

^[1]; Yu, Yan ^[2]; ^[1]; Srebnik, Simcha ^[1]; ^[3]; ^[1]

Univ. of British Columbia, Vancouver, BC (Canada)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Energy Research Scientific Computing Center (NERSC)

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725

OSTI ID:: 3002389

Journal Information:: Journal of Chemical Information and Modeling, Journal Name: Journal of Chemical Information and Modeling Journal Issue: 21 Vol. 65; ISSN 1549-9596; ISSN 1549-960X

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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