List of Publications


    2024

  1. Nordquist E, Jia Z, Chen J. Small molecule NS11021 promotes BK channel activation by increasing inner pore hydration. J. Chem. Inf. Model. 2024 (submitted) bioRxiv DOI: 10.1101/2024.06.03.597166
  2. Nordquist E#, Zhang M#, Kumar A, MacKerell A. Combined physics- and machine-learning-based method to identify druggable binding sites using SILCS-Hotspots. J. Comput. Aid. Mol. Des. 2024 (submitted) chemRxiv DOI: 10.26434/chemrxiv-2024-hrqq9

  3. 2023

  4. Nordquist E#, Zhang G#, Barethiya S, Ji N, White K, Han L, Jia Z, Shi J, Cui J, and Chen J. Incorporating physics to overcome data scarcity in predictive modeling of protein function: a case study of BK channels. PLOS Comput. Biol. 2023 19(9): e1011460. DOI: 10.1371/journal.pcbi.1011460
  5. Zhang L#, Barethiya S#, Nordquist E, Chen J. Machine Learning Generation of Dynamic Protein Conformational Ensembles. Molecules 2023, 28(10), 4047. DOI: 10.3390/molecules28104047
  6. Nordquist E, Jia Z, Chen J. Inner pore hydration free energy controls the activation of big potassium channels. Biophys. J. 2023, 122, 1158-1167. DOI: 10.1016/j.bpj.2023.02.005 (Best of BJ 2023 issue!)

  7. 2022

  8. Nordquist E, Clerico E, Chen J, Gierasch L. Computationally-aided modeling of Hsp70-client interactions: past, present, and future. J. Phys. Chem. B, 2022, 126 (36), 6780–6791 DOI: 10.1021/acs.jpcb.2c03806
  9. Nordquist E#, Schultz S#, Chen J. Using metadynamics to explore the free energy of dewetting in biologically-relevant nanopores. J. Phys. Chem. B 2022, 126 (34), 6428-6437 DOI: 10.1021/acs.jpcb.2c04157

  10. 2021

  11. Nordquist E, English C, Clerico E, Sherman W, Gierasch L, and Chen J. Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones. PLOS Comput. Biol., 2021, 17 (11): e1009567. DOI: 10.1371/journal.pcbi.1009567 PubMed

  12. 2020

  13. Gong X, Chiricotto M, Liu X, Nordquist E, Feig M, Brooks C, Chen J. Accelerating the generalized born with molecular volume and solvent accessible surface area implicit solvent model using graphics processing units. J. Comput. Chem., 2020, 41, 830–838. DOI: 10.1002/jcc.26133 PubMed

#These authors contributed equally to the work.