The GlycoMIP user facility provides all‑atom molecular modeling and molecular dynamics simulations through a one‑of‑a‑kind virtual user facility.
To discuss potential collaborative modeling projects, please contact us through the User Portal.
GlycoMIP Modeling Capabilities
Overview
interacting with the human ACE2 receptor (red protein, pink glycans).
In support of the GlycoMIP mission, we are developing modeling tools and services that enable
advanced computational studies of glycomaterials.
- Online tools and downloadable files to predict the three‑dimensional structures of engineered polysaccharides
- Online services enabling molecular dynamics (MD) simulations of oligosaccharides
Description
Online modeling tools access an AMBER‑certified GPU cluster consisting of 48 NVIDIA RTX 2080 Ti GPUs (11 GB each), 2 TB DDR4 ECC memory, and 144 TB RAID‑6 storage.
Applications
- Three‑dimensional structure prediction using the GLYCAM/AMBER force field
- Molecular dynamics simulations in explicit solvent
Associated Resources
Synergistic resources may be available on a project‑dependent basis through existing capabilities and tools.
GLYCAM‑Web provides online computational tools for predicting the three‑dimensional structures of oligosaccharides and glycoproteins.
Current capabilities include:
- Oligosaccharide conformation modeling
- Glycoprotein three‑dimensional structure modeling
- Viewing structures online
- Downloading structure files
Status of Resources: Server hardware has been received.
User Access: A graphical user interface for automated modeling studies is under development.