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Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM)

The Journal of chemical physics, 2018-08, Vol.149 (8), p.084103-084103

2018

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Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network Analytic Methods

Frontiers in molecular biosciences, 2019-06, Vol.6, p.42-42

2019

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Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures

Biomolecules (Basel, Switzerland), 2021-11, Vol.11 (12), p.1788

2021

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Advances in milestoning. II. Calculating time-correlation functions from milestoning using stochastic path integrals

The Journal of chemical physics, 2018-08, Vol.149 (8), p.084104-084104

2018

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Simulated evolution of optimal network Hamiltonian models for 5 amyloid fibril topologies using a genetic algorithm

Biophysical journal, 2024-02, Vol.123 (3), p.548a-548a

2024

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Advances in milestoning. II. Calculating time-correlation functions frommilestoning using stochastic path integrals

The Journal of chemical physics, 2018-08, Vol.149 (8)

2018

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Investigating intracellular SIRT1 regulation mechanisms using molecular dynamics simulations and machine learning

Biophysical journal, 2024-02, Vol.123 (3), p.551a-551a

2024

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Simulated mechanical testing of amyloid fibril structures using molecular dynamics simulations with enhanced sampling

Biophysical journal, 2023-02, Vol.122 (3), p.138a-139a

2023

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Calculating Watson-Crick to Hoogsteen Transition Kinetics in DNA with Langevin Dynamics and Fokker-Planck Diffusion in Reduced Configuration Space

Biophysical journal, 2016-02, Vol.110 (3), p.404a-405a

2016

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A Smoluchowski Equation for Force-Modulated Chemistry in Single Molecule Pulling Experiments

Biophysical journal, 2015-01, Vol.108 (2), p.161a-161a

2015

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Predicting Reaction Products and Automating Reactive Trajectory Characterization in Molecular Simulations with Support Vector Machines

Journal of chemical information and modeling, 2019-05, Vol.59 (6)

2019

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Local Graph Stability in Exponential Family Random Graph Models

SIAM journal on applied mathematics, 2021-01, Vol.81 (4), p.1389-1415

2021

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Predicting Reaction Products and Automating Reactive Trajectory Characterization in Molecular Simulations with Support Vector Machines

Journal of chemical information and modeling, 2019-06, Vol.59 (6), p.2753-2764

2019

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Reconstructing atomistic structures from residue-level protein structure networks using artificial neural networks

Biophysical journal, 2022-02, Vol.121 (3), p.133a-133a

2022

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Foregrounding the Code: Computational Chemistry Instructional Activities Using a Highly Readable Fluid Simulation Code

Journal of chemical education, 2023-03, Vol.100 (3), p.1155-1163

2023

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m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

Nature structural & molecular biology, 2016-09, Vol.23 (9), p.803

2016

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Network-Based Classification and Modeling of Amyloid Fibrils

The journal of physical chemistry. B, 2019-07, Vol.123 (26), p.5452-5462

2019

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Algorithms for Parameterizing Network Hamiltonians for Simulations of Amyloid Fibril Self-assembly

Biophysical journal, 2020-02, Vol.118 (3), p.306a-306a

2020

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Network-Based Modeling of Amyloid Fibril Formation

Biophysical journal, 2019-02, Vol.116 (3), p.559a-559a

2019

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Network Hamiltonian models reveal pathways to amyloid fibril formation

Scientific reports, 2020-09, Vol.10 (1), p.15668, Article 15668

2020

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Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

Grazioli, Gianmarc

2016

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Structural requirements for time-dependent and time-independent inhibition of prostaglandin synthase I (COX-1)

Johns, Gianmarc Grazioli

2007

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Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM)

Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network Analytic Methods

Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures

Advances in milestoning. II. Calculating time-correlation functions from milestoning using stochastic path integrals

Simulated evolution of optimal network Hamiltonian models for 5 amyloid fibril topologies using a genetic algorithm

Advances in milestoning. II. Calculating time-correlation functions frommilestoning using stochastic path integrals

Investigating intracellular SIRT1 regulation mechanisms using molecular dynamics simulations and machine learning

Simulated mechanical testing of amyloid fibril structures using molecular dynamics simulations with enhanced sampling

Calculating Watson-Crick to Hoogsteen Transition Kinetics in DNA with Langevin Dynamics and Fokker-Planck Diffusion in Reduced Configuration Space

A Smoluchowski Equation for Force-Modulated Chemistry in Single Molecule Pulling Experiments

Predicting Reaction Products and Automating Reactive Trajectory Characterization in Molecular Simulations with Support Vector Machines

Local Graph Stability in Exponential Family Random Graph Models

Predicting Reaction Products and Automating Reactive Trajectory Characterization in Molecular Simulations with Support Vector Machines

Reconstructing atomistic structures from residue-level protein structure networks using artificial neural networks

Foregrounding the Code: Computational Chemistry Instructional Activities Using a Highly Readable Fluid Simulation Code

m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

Network-Based Classification and Modeling of Amyloid Fibrils

Algorithms for Parameterizing Network Hamiltonians for Simulations of Amyloid Fibril Self-assembly

Network-Based Modeling of Amyloid Fibril Formation

Network Hamiltonian models reveal pathways to amyloid fibril formation

Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

Structural requirements for time-dependent and time-independent inhibition of prostaglandin synthase I (COX-1)

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