Zachary Smith

发表

Confronting pitfalls of AI-augmented molecular dynamics using statistical physics

E. Tajkhorshid, P. Tiwary, S. Pant, 2020, bioRxiv.

Discovering loop conformational flexibility in T4 lysozyme mutants through artificial intelligence aided molecular dynamics

P. Tiwary, Zachary Smith, Yihang Wang, 2020, bioRxiv.

A statistical physics based approach to capture spurious solutions in AI-enhanced molecular dynamics

E. Tajkhorshid, P. Tiwary, S. Pant, 2020 .

Reaction coordinates and rate constants for liquid droplet nucleation: Quantifying the interplay between driving force and memory.

P. Tiwary, Zachary Smith, Sun-Ting Tsai, 2019, The Journal of chemical physics.

Can one trust kinetic and thermodynamic observables from biased metadynamics simulations: detailed quantitative benchmarks on millimolar drug fragment dissociation

P. Tiwary, Zachary Smith, A. Kells, 2019, bioRxiv.

Discovering Protein Conformational Flexibility Through Artificial Intelligence Aided Molecular Dynamics.

Yihang Wang, Pratyush Tiwary, Pavan Ravindra, 2020, The journal of physical chemistry. B.

SGOOP-d: Estimating Kinetic Distances and Reaction Coordinate Dimensionality for Rare Event Systems from Biased/Unbiased Simulations.

P. Tiwary, Zachary Smith, Sun-Ting Tsai, 2021, Journal of chemical theory and computation.

Automatic mutual information noise omission (AMINO): generating order parameters for molecular systems

Zachary Smith, Pratyush Tiwary, Pavan Ravindra, 2019, bioRxiv.

Protein flexibility and dissociation pathway differentiation can explain onset of resistance mutations in kinases

M. Seeliger, M. Shekhar, P. Tiwary, 2021, bioRxiv.

Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization

Pratyush Tiwary, Sun-Ting Tsai, Debabrata Pramanik, 2018, bioRxiv.

Computational growth model of breast microcalcification clusters in simulated mammographic environments

Zachary Smith, Andre Khalil, Shayne M. Plourde, 2016, Comput. Biol. Medicine.

Enhanced Sampling with Machine Learning: A Review

P. Tiwary, Zachary Smith, Lukas Herron, 2023, Annual review of physical chemistry.

Making High-Dimensional Molecular Distribution Functions Tractable through Belief Propagation on Factor Graphs.

P. Tiwary, Zachary Smith, 2021, The journal of physical chemistry. B.

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

P. Tiwary, Zachary Smith, Bodhi P. Vani, 2023, bioRxiv.

Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations?: Detailed Quantitative Benchmarks on Millimolar Drug Fragment Dissociation.

P. Tiwary, Zachary Smith, A. Kells, 2019, The journal of physical chemistry. B.

Reaction coordinates and rate constants for liquid droplet nucleation: Quantifying the interplay between driving force and memory.

P. Tiwary, Zachary Smith, Sun-Ting Tsai, 2019, The Journal of chemical physics.