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The Journal of Physical Chemistry. B|September 29, 2021
Making High-Dimensional Molecular Distribution Functions Tractable through Belief Propagation on Factor GraphsZachary Smith, Pratyush TiwaryJournal of Chemical Theory and Computation|October 18, 2021
SGOOP-d: Estimating Kinetic Distances and Reaction Coordinate Dimensionality for Rare Event Systems from Biased/Unbiased SimulationsSun-Ting Tsai, Zachary Smith, Pratyush TiwaryThe Journal of Chemical Physics|October 24, 2019
Reaction coordinates and rate constants for liquid droplet nucleation: Quantifying the interplay between driving force and memorySun-Ting Tsai, Zachary Smith, Pratyush TiwaryThe Journal of Physical Chemistry. B|April 13, 2019
Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations?: Detailed Quantitative Benchmarks on Millimolar Drug Fragment DissociationDebabrata Pramanik, Zachary Smith, Adam Kells, et al.The Journal of Chemical Physics|December 24, 2018
Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorizationZachary Smith, Debabrata Pramanik, Sun-Ting Tsai, et al.Angewandte Chemie (International Ed. in English)|April 29, 2022
Protein Flexibility and Dissociation Pathway Differentiation Can Explain Onset of Resistance Mutations in KinasesMrinal Shekhar, Zachary Smith, Markus A Seeliger, et al.Journal of Chemical Information and Modeling|March 7, 2024
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with AttentionZachary Smith, Michael Strobel, Bodhi P Vani, et al.Biorxiv : the Preprint Server for Biology|August 7, 2023
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with AttentionZachary Smith, Michael Strobel, Bodhi P Vani, et al.Annual Review of Physical Chemistry|February 21, 2024
Enhanced Sampling with Machine LearningShams Mehdi, Zachary Smith, Lukas Herron, et al.The Journal of Chemical Physics|December 23, 2020
Confronting pitfalls of AI-augmented molecular dynamics using statistical physicsShashank Pant, Zachary Smith, Yihang Wang, et al.Pageof 21