Rapid Computational Identification of Therapeutic Targets for Pathogens

Jonathan Allen | 20-ERD-062

Executive Summary

We will develop a computational drug target identification tool, which links previous knowledge of proteins and their drug target potential to rapidly guide countermeasure design in newly sequenced pathogen genomes. Systematically inferring links between a new pathogen and previous countermeasure design efforts will create a rigorous system for prioritizing new countermeasures for biological threats.

Publications, Presentations, and Patents

Lau, E. Y., O. A. Negrete, W. F. D. Bennett, B. J. Bennion, M. Borucki, F. Bourguet, A. Epstein, et al. 2021. "Discovery of Small-Molecule Inhibitors of Sars-Cov-2 Proteins Using a Computational and Experimental Pipeline." Front Mol Biosci 8 (2021): 678701. https://doi.org/10.3389/fmolb.2021.678701. https://www.ncbi.nlm.nih.gov/pubmed/34327214.

Posada, Randy, Mary Silva, Marisa Torres, Jonathan Allen, Jeff Drocco, Sarah Sandholtz, and Adam Zemla. 2022. "Graph-Based Featurization Methods for Classifying Small Molecule Compounds." UC Merced Undergraduate Research Journal 14(1). https://doi.org/https://doi.org/10.5070/m414157338.

Shim, Heesung, Hyojin Kim, Jonathan E. Allen, and Heike Wulff. 2022. "Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel–Ligand Docking." Journal of Chemical Information and Modeling 62, no. 10 (2022/05/23 2022): 2301-15. https://doi.org/10.1021/acs.jcim.1c01510. https://doi.org/10.1021/acs.jcim.1c01510.

Stevenson, Garrett A., Derek Jones, Hyojin Kim, W. F. Drew Bennett, Brian J. Bennion, Monica Borucki, Feliza Bourguet, et al. "High-Throughput Virtual Screening of Small Molecule Inhibitors for Sars-Cov-2 Protein Targets with Deep Fusion Models." In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'21), St. Louis, MO. Nov. 2021.

Zemla, Adam T., Jonathan E. Allen, Dan Kirshner, and Felice C. Lightstone. "Pdbspheres - a Method for Finding 3d Similarities in Local Regions in Proteins." Nucleic Acids Res. Accepted. 2022: 2022.01.04.474934. https://doi.org/10.1101/2022.01.04.474934. https://www.biorxiv.org/content/biorxiv/early/2022/05/14/2022.01.04.474….