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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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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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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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Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment

Journal of the American Chemical Society, 2012-08, Vol.134 (30), p.12565-12577

2012

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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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Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction

Nature communications, 2022-01, Vol.13 (1), p.350-350, Article 350

2022

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De novo structure prediction and experimental characterization of folded peptoid oligomers

Proceedings of the National Academy of Sciences - PNAS, 2012-09, Vol.109 (36), p.14320-14325

2012

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Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na+/K+-ATPase ion selectivity

The Journal of biological chemistry, 2017-07, Vol.292 (30), p.12412-12423

2017

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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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A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models

Biophysical journal, 2014-03, Vol.106 (6), p.1359-1370

2014

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Precisely tuneable energy transfer system using peptoid helix-based molecular scaffold

Scientific reports, 2017-07, Vol.7 (1), p.4786-10, Article 4786

2017

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Reconciling Simulations and Experiments With BICePs: A Review

Frontiers in molecular biosciences, 2021-05, Vol.8, p.661520-661520

2021

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Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER

Biopolymers, 2011, Vol.96 (5), p.639-650

2011

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Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment

Journal of the American Chemical Society, 2010-04, Vol.132 (13), p.4702-4709

2010

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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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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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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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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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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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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)

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

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

Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment

Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides

Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction

De novo structure prediction and experimental characterization of folded peptoid oligomers

Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na+/K+-ATPase ion selectivity

Adaptive Markov state model estimation using short reseeding trajectories

A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models

Precisely tuneable energy transfer system using peptoid helix-based molecular scaffold

Reconciling Simulations and Experiments With BICePs: A Review

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER

Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment

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

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

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

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

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

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