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Zachary Smith
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Year
Automatic mutual information noise omission (AMINO): generating order parameters for molecular systems
P Ravindra, Z Smith, P Tiwary
Molecular Systems Design & Engineering 5 (1), 339-348, 2020
442020
Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization
Z Smith, D Pramanik, ST Tsai, P Tiwary
The Journal of Chemical Physics 149 (23), 2018
402018
Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations?: Detailed Quantitative Benchmarks on Millimolar Drug Fragment Dissociation
D Pramanik, Z Smith, A Kells, P Tiwary
The Journal of Physical Chemistry B 123 (17), 3672-3678, 2019
382019
Protein flexibility and dissociation pathway differentiation can explain onset of resistance mutations in kinases
M Shekhar, Z Smith, MA Seeliger, P Tiwary
Angewandte Chemie International Edition 61 (28), e202200983, 2022
302022
SGOOP-d: Estimating kinetic distances and reaction coordinate dimensionality for rare event systems from biased/unbiased simulations
ST Tsai, Z Smith, P Tiwary
Journal of Chemical Theory and Computation 17 (11), 6757-6765, 2021
252021
Reaction coordinates and rate constants for liquid droplet nucleation: Quantifying the interplay between driving force and memory
ST Tsai, Z Smith, P Tiwary
The Journal of Chemical Physics 151 (15), 154106, 2019
252019
Discovering Protein Conformational Flexibility through Artificial-Intelligence-Aided Molecular Dynamics
Z Smith, P Ravindra, Y Wang, R Cooley, P Tiwary
The Journal of Physical Chemistry B 124 (38), 8221-8229, 2020
242020
Confronting pitfalls of AI-augmented molecular dynamics using statistical physics
S Pant, Z Smith, Y Wang, E Tajkhorshid, P Tiwary
The Journal of Chemical Physics 153 (23), 2020
172020
Enhanced Sampling with Machine Learning
S Mehdi, Z Smith, L Herron, Z Zou, P Tiwary
Annual Review of Physical Chemistry 75, 2024
9*2024
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention
Z Smith, M Strobel, BP Vani, P Tiwary
bioRxiv, 2023
32023
Toward Ensemble-Based Drug Discovery Through Enhanced Sampling
Z Smith
University of Maryland, College Park, 2023
2023
Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs
Z Smith, P Tiwary
The Journal of Physical Chemistry B 125 (40), 11150-11158, 2021
2021
An efficient approach to computing drug-target residence times by combining enhanced sampling methods
D Lupyan, D Braduardi, P Tiwary, Z Smith, G Krilov
APS March Meeting Abstracts 2021, Y26. 002, 2021
2021
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Articles 1–13