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Adaptive Markov state model estimation using short reseeding trajectories

The Journal of chemical physics, 2020-01, Vol.152 (2), p.024103-024103

2020

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BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations

Journal of chemical information and modeling, 2023-04, Vol.63 (8), p.2370-2381

2023

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Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models

Biophysical journal, 2017-08, Vol.113 (4), p.785-793

2017

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Estimation of binding rates and affinities from multiensemble Markov models and ligand decoupling

The Journal of chemical physics, 2022-04, Vol.156 (13), p.134115

2022

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SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

Nature chemistry, 2021-07, Vol.13 (7), p.651-659

2021

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Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)

Journal of the American Chemical Society, 2010-02, Vol.132 (5), p.1526-1528

2010

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Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization

The journal of physical chemistry. B, 2018-05, Vol.122 (21), p.5610-5622

2018

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Folding@home: Achievements from over 20 years of citizen science herald the exascale era

Biophysical journal, 2023-07, Vol.122 (14), p.2852-2863

2023

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A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations

Journal of chemical theory and computation, 2016-12, Vol.12 (12), p.5768-5776

2016

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Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding

The journal of physical chemistry. B, 2023-12, Vol.127 (50), p.10682-10690

2023

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Markov State Models to Elucidate Ligand Binding Mechanism

Methods in molecular biology (Clifton, N.J.), 2021, Vol.2266, p.239

2021

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Reconciling Simulated Ensembles of Apomyoglobin with Experimental Hydrogen/Deuterium Exchange Data Using Bayesian Inference and Multiensemble Markov State Models

Journal of chemical theory and computation, 2020-02, Vol.16 (2), p.1333-1348

2020

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Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85

Journal of the American Chemical Society, 2011-02, Vol.133 (4), p.664-667

2011

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Effects of Salinity and Temperature on the Flexibility and Function of a Polyextremophilic Enzyme

International journal of molecular sciences, 2022-12, Vol.23 (24), p.15620

2022

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Solution-State Preorganization of Cyclic β‑Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2

Journal of chemical information and modeling, 2021-05, Vol.61 (5), p.2353-2367

2021

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Taming the complexity of protein folding

Current opinion in structural biology, 2011-02, Vol.21 (1), p.4-11

2011

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Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential

The journal of physical chemistry. B, 2015-12, Vol.119 (50), p.15407-15417

2015

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Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

Journal of chemical theory and computation, 2021-10, Vol.17 (10), p.6536-6547

2021

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Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

Journal of the American Chemical Society, 2011-11, Vol.133 (45), p.18413-18419

2011

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Atomistic folding simulations of the five-helix bundle protein λ(6−85)

Journal of the American Chemical Society, 2011-02, Vol.133 (4), p.664-667

2011

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Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α‑Helix Folding

The journal of physical chemistry. B, 2016-02, Vol.120 (5), p.926-935

2016

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Microcanonical coarse-graining of the kinetic Ising model

The Journal of chemical physics, 2020-02, Vol.152 (8), p.084104

2020

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Exposing the Nucleation Site in α‑Helix Folding: A Joint Experimental and Simulation Study

The journal of physical chemistry. B, 2019-02, Vol.123 (8), p.1797-1807

2019

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Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides

Journal of chemical information and modeling, 2015-04, Vol.55 (4), p.806-813

2015

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Bayesian inference of conformational state populations from computational models and sparse experimental observables

Journal of computational chemistry, 2014-11, Vol.35 (30), p.2215-2224

2014

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Adaptive Markov state model estimation using short reseeding trajectories

BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations

Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models

Estimation of binding rates and affinities from multiensemble Markov models and ligand decoupling

SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)

Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization

Folding@home: Achievements from over 20 years of citizen science herald the exascale era

A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations

Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding

Markov State Models to Elucidate Ligand Binding Mechanism

Reconciling Simulated Ensembles of Apomyoglobin with Experimental Hydrogen/Deuterium Exchange Data Using Bayesian Inference and Multiensemble Markov State Models

Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85

Effects of Salinity and Temperature on the Flexibility and Function of a Polyextremophilic Enzyme

Solution-State Preorganization of Cyclic β‑Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2

Taming the complexity of protein folding

Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential

Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

Atomistic folding simulations of the five-helix bundle protein λ(6−85)

Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α‑Helix Folding

Microcanonical coarse-graining of the kinetic Ising model

Exposing the Nucleation Site in α‑Helix Folding: A Joint Experimental and Simulation Study

Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides

Bayesian inference of conformational state populations from computational models and sparse experimental observables

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