Research

Computational chemistry, medicinal chemistry, and machine learning.  I develop machine-learning models - 3D convolutional neural networks - for docking-pose classification to enable improved high-throughput virtual screening.  I also generate atomistic-resolution protein structural models and dock small molecules to these models to understand molecular mechanisms of action. I'm also interested in structure/ligand-based drug design.

PhD Chemistry, University of California, Davis, 2019

BS Chemistry, University of California, Davis, 2012

Kim H, Shim H, Ranganath A, He S, Stevenson G, Allen JE. Protein-ligand binding affinity prediction using multi-instance learning with docking structures. Front Pharmacol. 2025 Jan 3;15:1518875. doi: 10.3389/fphar.2024.1518875. PMID: 39830331; PMCID: PMC11738626.

Nasburg JA, Rouen KC, Dietrich CJ, Shim H, Zhang M, Vorobyov I, Wulff H. 6,7-Dichloro-1H-indole-2,3-dione-3-oxime functions as a superagonist for the intermediateconductance Ca2+-activated K+ channel KCa3.1. Mol Pharmacol. 2025 Mar;107(3):100018. doi: 10.1016/j.molpha.2025.100018. Epub 2025 Jan 31. PMID: 40068526.

Wong BHS, Shim H, Goay SSM, Ong ST, Muhammad Taib NAB, Chai KXY, Lim K, Huang D, Ong CK, Vaiyapuri TS, Cheah YC, Wang Y, Wulff H, Webster RD, Shelat VG, Verma NK. The novel quinoline derivative SKA-346 as a KCa3.1 channel selective activator. RSC Adv. 2024 Dec 4;14(52):38364-38377. doi: 10.1039/d4ra07330d. PMID: 39635364; PMCID: PMC11615718.

Shim, H.; Allen, J.E.; Bennett, W.F.D. Enhancing Docking Accuracy with PECAN2, a 3D Atomic Neural Network Trained without Co-Complex Crystal Structures. Mach. Learn. Knowl. Extr. 2024, 6, 642-657. https://doi.org/10.3390/make6010030

Atomwise AIMS Program. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep. 2024 Apr 2;14(1):7526. doi: 10.1038/s41598-024-54655-z. PMID: 38565852; PMCID: PMC10987645.

Kyllo T, Singh V, Shim H, Latika S, Nguyen HM, Chen YJ, Terry E, Wulff H, Erickson JD. Riluzole and novel naphthalenyl substituted aminothiazole derivatives prevent acute neural excitotoxic injury in a rat model of temporal lobe epilepsy. Neuropharmacology. 2023 Feb 15;224:109349.

Rivera, A.; Nasburg, J.; Shim, H.; Shmukler, B.; Kitten, J.; Wohlgemuth, J.; Dlott, J.; Snyder, L.; Brugnara, C.; Wulff, H.; Alper, S., The erythroid K-Cl cotransport inhibitor [(Dihydroindenyl)oxy]acetic acid (DIOA) blocks erythroid Ca2+-activated K+ channel KCNN4. American Journal of Physiology-Cell Physiology, 2022 Sep 1;323(3):C694- C705.

Shim H, Kim H, Allen J, Wulff H. Pose Classification using 3D Atomic Structure-Based Neural Networks Applied to Ion Channel-Ligand Docking. To appear in ACS J Chem Inf Model, 2022, 10.1021/acs.jcim.1c01510.

Brown, B. M.; Shim, H.; Christophersen, P.; Wulff, H., Pharmacology of Small- and Intermediate-Conductance Ca2+-Activated K+ Channels. Annual Reviews in Pharmacology , 2020, Jan 6;60:219-240.

Ong,S.; Ng,A.; Ng,X.; Zhuang,Z.; Wong,B.; Prasannan,P.; Kok,Y.; Bi,X.; Shim,H.; Wulff,H.; Chandy,K.G.; Verma,N., Extracellular K+ Dampens T Cell Functions: Implications for Immune Suppression in the Tumor Microenvironment. Bioelectricity, 2019, 1:3, 169-179

Shim, H.; Brown, B. M.; Singh, L.; Singh, V.; Fettinger, J. C.; Yarov-Yarovoy, V.; Wulff, H. The trials and tribulations of structure assisted design of KCa channel activators. Frontiers in Pharmacology, 2019, Sep 20;10:972

Brown, B. M.; Shim, H.; Zhang, M.; Yarov-Yarovoy, V.; Wulff, H. Structural Determinants for the Selectivity of the Positive KCa3.1 Gating Modulator 5-Methylnaphtho[2,1- d]oxazol-2-amine (SKA-121). Molecular Pharmacology 2017, 92 (4), 469-480.

Brown, B. M.; Shim, H.; Wulff, H. Are there superagonists for calcium-activated potassium channels? Channels (Austin) 2017, 11 (6), 504- 506.