Publications

2025

Nordquist E, Zhang M, Yu W, MacKerell A. Computational modeling of PROTAC ternary complexes as ensembles using SILCS-PROTAC. J. Med. Chem. (submitted) 2025. ChemRxiv
Patel R, Nordquist E, Polli J. Prediction of surfactant-mediated dissolution of poorly soluble drugs from drug powder. Eur. J. Pharm. Sci. 2025, 107052. DOI

Nordquist E^#, Zhang M^#, Kumar A, MacKerell A. Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots. J. Chem. Inf. Model. 2024, 64, 19, 7743–7757. DOI PubMed ChemRxiv
Nordquist E, Jia Z, Chen J. Small molecule NS11021 promotes BK Channel Activation by Increasing Inner Pore Hydration. J. Chem. Inf. Model. 2024, 64, 19, 7616–7625. DOI PubMed bioRxiv

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 PubMed
Zhang L^#, Barethiya S^#, Nordquist E, Chen J. Machine learning generation of dynamic protein conformational ensembles. Molecules 2023, 28(10), 4047. DOI PubMed
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 PubMed Best of Biophys J

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 PubMed
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 PubMed

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 PubMed

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 PubMed

Nordquist E, Horrigan F, MacKerell A. Computational ligand binding site prediction. Springer Nature (accepted) 2025.

^#These authors contributed equally to the work.