Modeling Services

The GlycoMIP user facility will provide all-atom molecular modeling and molecular dynamics simulations through a one-of-a-kind virtual user facility.

Overview

A molecular dynamics simulation of the SARS-CoV-2 spike glycoprotein (silver protein, grey glycans) in complex with the human ACE2 receptor (red protein, pink glycans).

In support of the GlycoMIP mission, we are developing:

  • Online tools and downloadable files that will enable users to predict the 3D structures of engineered polysaccharides
  • Online services to enable the MD simulation of oligosaccharides

Description

Online modeling tools will access an AMBER Certified GPU Cluster (48 NVIDIA RTX 2080 Ti 11GB GPU, 2TB DDR4 2666MHz ECC REG Memory, 144 TB AID 6 storage)

Applications

  • 3D structure prediction using the GLYCAM/AMBER Force Field.
  • Molecular dynamics (MD) simulation in explicit solvent

Associated Resources

Synergistic resources will be available, on a project-dependent basis, through existing capabilities and tools.  GLYCAM-Web provides online computational tools predicting the 3D shapes of oligosaccharides and glycoproteins.

Current capabilities include:

  • Oligosaccharide conformation modeling
  • Glycoprotein 3D structure Modeling
  • View structures online
  • Download structure files

Status of Resources:  TBD

User Access:  Under development