NERSCPowering Scientific Discovery for 50 Years

Structure Refinement of the Spike Protein of SARS-COV-2

Award from the COVID-19 HPC Consortium

Ching Wai Yum

Wai-Yim Ching is a Professor in the Dept. of Physics and Astronomy at the U. of Missouri-Kansas City.

Investigator: Wai-Yim Ching
Affiliation: University of Missouri-Kansas City

The current COVID-19 pandemic is a severe threat in human health leading to social, and economic disruption in the entire world. The spike (S) glycoprotein of SARS-COV-2 is considered to be a key target for vaccine development since it makes first contact to ACE2 acceptor in human protein. The structure of the spike protein was recently determined by cryo-EM techniques with a resolution of 3.5 Å. It contains three chains and each chain consists of four structural domains: receptor binding domain (RBD), n-terminal domain (NTD), subdomain 1 and 2 (SD1-SD2) and S2.

WYChing covid cover

This project’s research is featured on the cover of PCCP.

This project will refine the structures of these domains to much higher accuracy using large scale ab initio simulations and investigate their atomic scale interaction and intra molecular binding mechanism. They will also present electronic structure calculations with detailed intra and intermolecular interactions of the spike protein in the pre- and post-fusion configuration which are difficult to determine experimentally. In addition, they are studying the further interaction between the spike protein and ACE2 to shed some light on the genetic modification due to mutation and thereby provide useful insights for various vaccine development and drug design.


  •  Intra- and intermolecular atomic-scale interactions in the receptor binding domain of SARS-CoV-2 spike protein: implication for ACE2 receptor binding, Adhikari, Puja and Li, Neng and Shin, Matthew and Steinmetz, Nicole F. and Twarock, Reidun and Podgornik, Rudolf and Ching, Wai-Yim. Phys. Chem. Chem. Phys., 2020, DOI: 10.1039/D0CP03145C
  • Amino acid interacting network in the receptor
    binding domain of SARS-CoV-2 spike protein, Adhikari, Puja and Ching, Wai-Yim, RSC( Royal Society of Chemistry) Advances, 2020, 10, 39831, DOI: 10.1039/d0ra08222h


About NERSC and Berkeley Lab
The National Energy Research Scientific Computing Center (NERSC) is a U.S. Department of Energy Office of Science User Facility that serves as the primary high performance computing center for scientific research sponsored by the Office of Science. Located at Lawrence Berkeley National Laboratory, NERSC serves almost 10,000 scientists at national laboratories and universities researching a wide range of problems in climate, fusion energy, materials science, physics, chemistry, computational biology, and other disciplines. Berkeley Lab is a DOE national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California for the U.S. Department of Energy. »Learn more about computing sciences at Berkeley Lab.