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Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

Proceedings of the National Academy of Sciences - PNAS, 2012-07, Vol.109 (29), p.11681-11686

2012

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Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

The Journal of chemical physics, 2012-10, Vol.137 (13), p.134111-134111

Bowman, Gregory R

2012

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The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

Nature communications, 2021-03, Vol.12 (1), p.1936-1936, Article 1936

2021

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Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

Accounts of chemical research, 2020-03, Vol.53 (3), p.654-661

2020

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A role for both conformational selection and induced fit in ligand binding by the LAO protein

PLoS computational biology, 2011-05, Vol.7 (5), p.e1002054

2011

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Discovery of multiple hidden allosteric sites by combining Markov state models and experiments

Proceedings of the National Academy of Sciences - PNAS, 2015-03, Vol.112 (9), p.2734-2739

2015

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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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Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

Nature chemistry, 2014-01, Vol.6 (1), p.15-21

2014

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Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant

Structure (London), 2016-10, Vol.24 (10), p.1719-1728

2016

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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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Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

Biophysical journal, 2012-01, Vol.102 (2), p.315-324

2012

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Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Nature communications, 2023-03, Vol.14 (1), p.1177-1177, Article 1177

2023

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Protein folded states are kinetic hubs

Proceedings of the National Academy of Sciences - PNAS, 2010-06, Vol.107 (24), p.10890-10895

2010

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Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets

Nature communications, 2021-05, Vol.12 (1), p.3023-3023, Article 3023

2021

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Modelling proteins’ hidden conformations to predict antibiotic resistance

Nature communications, 2016-10, Vol.7 (1), p.12965-12965, Article 12965

2016

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Exploiting a natural conformational switch to engineer an interleukin-2 ‘superkine’

Nature (London), 2012-04, Vol.484 (7395), p.529-533

2012

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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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The intrinsically disordered protein TgIST from Toxoplasma gondii inhibits STAT1 signaling by blocking cofactor recruitment

Nature communications, 2022-07, Vol.13 (1), p.4047-4047, Article 4047

2022

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Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation

Accounts of chemical research, 2015-04, Vol.48 (4), p.1098-1105

2015

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Rapid equilibrium sampling initiated from nonequilibrium data

Proceedings of the National Academy of Sciences - PNAS, 2009-11, Vol.106 (47), p.19765-19769

2009

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Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer

Nature structural & molecular biology, 2017-01, Vol.24 (1), p.69-76

2017

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Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators

PloS one, 2017-06, Vol.12 (6), p.e0178678

2017

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Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation

Science signaling, 2020-01, Vol.13 (615)

2020

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A cryptic pocket in Ebola VP35 allosterically controls RNA binding

Nature communications, 2022-04, Vol.13 (1), p.2269-10, Article 2269

2022

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Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding

eLife, 2018-10, Vol.7

2018

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Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

A role for both conformational selection and induced fit in ligand binding by the LAO protein

Discovery of multiple hidden allosteric sites by combining Markov state models and experiments

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

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant

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

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Protein folded states are kinetic hubs

Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets

Modelling proteins’ hidden conformations to predict antibiotic resistance

Exploiting a natural conformational switch to engineer an interleukin-2 ‘superkine’

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

The intrinsically disordered protein TgIST from Toxoplasma gondii inhibits STAT1 signaling by blocking cofactor recruitment

Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation

Rapid equilibrium sampling initiated from nonequilibrium data

Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer

Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators

Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation

A cryptic pocket in Ebola VP35 allosterically controls RNA binding

Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding

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