Matthew Smith

Overview

Titles

Postdoctoral Research Scientist

Email
ms7434@cumc.columbia.edu

Lab

Barry Honig

Matthew Smith is a postdoctoral research scientist in the lab of Barry Honig. His research broadly focuses on the interactions between small molecules and proteins. In the Honig Lab, he is using structural bioinformatics to study protein-compound interactions involving metabolites in different disease states, like cancer. He previously worked in small-molecule drug discovery, using computational chemistry methods like ultra-large-scale molecular docking, chemoinformatics, and molecular dynamics simulations. His PhD work involved modeling and predicting direct ligand-ligand interactions between positron emission tomography (PET) radiotracers binding to protein fibrils associated with neurodegenerative diseases like Alzheimer's. Before graduate school in biophysics, he studied math and biostatistics.

Education History

PhD, University of California, San Francisco- Biophysics

MPH, Yale University- Biostatistics

BS, Yale University- Mathematics

Publications

Smith MS *, DeGrado WF, Grabe M, Shoichet BK. A Cooperative Model for Symmetric Ligand Binding to Protein Fibrils. Biochemistry 2025,64,3382-3392. 2025 July 23

Liu F, Mailhot O, Glenn IS, Vigneron SF, Bassim V, Xu X, Fonseca-Valencia K, Smith MS, Radchenko DS, Fraser JS, Moroz YS, Irwin JJ, Shoichet BK. The impact of library size and scale of testing on virtual screening. Nature Chemical Biology. 2025 Jan 3.

Kunach P, Vaquer-Alicea J, Smith MS, Monistrol J, Hopewell R, Moquin L, Therriault J, Tissot C, Rahmouni N, Massarweh G, Soucy J-P, Guiot M-C, Shoichet BK, Rosa-Neto P, Diamond MI, Shahmoradian SH. Cryo-EM structure of Alzheimer’s disease tau filaments with PET ligand MK-6240. Nature Communications 15, 8497 (2024). 

Smith MS*, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JI, DeGrado WF, Shoichet BK. Docking for Molecules That Bind in a Symmetric Stack with SymDOCK. Journal of Chemical Information and Modeling. 2024,64,2,425–434. 2024 Jan 8. 

Gu S, Smith MS*, Yang Y, Irwin JJ, Shoichet BK. Ligand Strain Energy in Large Library Docking. Journal of Chemical Information and Modeling. 2021,61,9,4331–4341. 2021 Sep 1. 

Smith MS*, Devarajan K. Probability-based methods for outlier detection in replicated high-throughput biological data. bioRxiv. 2020 August 7.