Yi He

Assistant Professor

Chemical Biology and Biochemistry
Physical Chemistry
Theoretical and Computational Chemistry

Contact Information

Phone: 505 277-6655


  • B.S. in Physics, 2003, Huazhong University of Science and Technology 
  • B.E. in Computer Science, 2003, Huazhong University of Science and Technology 
  • Ph.D. in Biophysics, 2009, Huazhong University of Science and Technology 
  • Postdoctoral Associate in Chemistry, 2009-2012, Cornell University 
  • Research Associate  in Chemistry, 2012-2017, Cornell University 
  • Research Scientist in Bioengineering, 2017-2018, University of California Merced


Developments of Computational Approaches to Characterize Flexible Proteins

Prediction of biological function related structure ensembles of flexible proteins, such as Intrinsically Disordered Proteins (IDPs), using machine learning algorithms, coarse-grained modeling, all-atom modeling and experimental data. This project provides detailed information which is beneficial for drug and protein-based biosensor design.

Simulating Dynamics and Interactions of Large Biomolecular Systems

Using customized physics-based coarse-grained models of proteins and nucleic acids to simulate dynamics and the interacting process of large biomolecular complexes comparable to experimental timescales.

Protein Structure Prediction

Developing algorithms and pipelines using a combination of knowledge-based and physics-based protein structure prediction approaches.

Developments of Physics-based Multiscale Computational Models

Construct coarse-grained computational models based on the free energy landscape derived from quantum or all-atom calculations to simulate different systems of interests. 

Selected Publications

  1. Y He, Suhani Nagpal, Mourad Sadqi, Eva de Alba, Victor Muñoz – Glutton: A tool for generating structural ensembles of partly disordered proteins from chemical shifts, Bioinformatics, (under review, 2018)
  2. Y He, S Rackovsky, Y Yin, HA Scheraga – Alternative approach to protein structure prediction based on sequential similarity of physical properties. Proc. Natl. Acad. Sci., U.S.A., 112, 5029-5032 (2015). 
  3. Y He, M Maciejczyk, S Ołdziej, HA Scheraga, A Liwo – Mean-field interactions between nucleic acid base dipoles drive formation of the double helix, Phys. Rev. Lett., 110, 098101 (2013)A Liwo, Y He, HA Scheraga Coarse-grained force field: general folding theory, Phys. Chem. Chem. Phys., 13 (38), 16890-16901 (2011)
  4. A Liwo, Y He, HA Scheraga Coarse-grained force field: general folding theory, Phys. Chem. Chem. Phys., 13 (38), 16890-16901 (2011) 
  5. Y He, A Liwo, H Weinstein, HA Scheraga – PDZ Binding to the BAR domain of PICK1 is Elucidated by Coarse-grained Molecular Dynamics, J. Mol. Biol., 405, 298-314 (2011)