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Water in Cavity−Ligand Recognition

Journal of the American Chemical Society, 2010-09, Vol.132 (34), p.12091-12097

2010

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Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor

Proceedings of the National Academy of Sciences - PNAS, 2018-03, Vol.115 (12), p.3036-3041

2018

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Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor

Proceedings of the National Academy of Sciences - PNAS, 2016-10, Vol.113 (43), p.12162-12167

2016

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PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

Nucleic acids research, 2004-07, Vol.32 (Web Server issue), p.W665-W667

2004

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Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

Journal of chemical theory and computation, 2015-08, Vol.11 (8), p.3584-3595

2015

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Molecular dynamics simulations and drug discovery

BMC biology, 2011-10, Vol.9 (1), p.71-71, Article 71

2011

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Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

Quarterly reviews of biophysics, 2015-11, Vol.48 (4), p.479-487

2015

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Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

Molecular simulation, 2016-09, Vol.42 (13), p.1046-1055

2016

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A glycan gate controls opening of the SARS-CoV-2 spike protein

Nature chemistry, 2021-10, Vol.13 (10), p.963-968

2021

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G-protein coupled receptors: advances in simulation and drug discovery

Current opinion in structural biology, 2016-12, Vol.41 (C), p.83-89

2016

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Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV‑2 Main Protease

Journal of chemical information and modeling, 2021-07, Vol.61 (7), p.3495-3501

2021

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Molecular recognition and ligand association

Annual review of physical chemistry, 2013-01, Vol.64 (1), p.151-175

2013

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NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function

Journal of chemical information and modeling, 2011-11, Vol.51 (11), p.2897-2903

2011

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Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations

Journal of structural biology, 2019-06, Vol.206 (3), p.267-279

2019

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Ensemble Docking in Drug Discovery

Biophysical journal, 2018-05, Vol.114 (10), p.2271-2278

2018

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Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor

Biophysical journal, 2015-04, Vol.108 (7), p.1796-1806

2015

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Improvements to the APBS biomolecular solvation software suite

Protein science, 2018-01, Vol.27 (1), p.112-128

2018

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Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

Journal of chemical theory and computation, 2014-07, Vol.10 (7), p.2677-2689

2014

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Membrane Allostery and Unique Hydrophobic Sites Promote Enzyme Substrate Specificity

Journal of the American Chemical Society, 2018-03, Vol.140 (9), p.3285-3291

2018

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Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

Quarterly reviews of biophysics, 2012-02, Vol.45 (1), p.1-25

2012

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Accelerated molecular dynamics simulations of protein folding

Journal of computational chemistry, 2015-07, Vol.36 (20), p.1536-1549

2015

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Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

The Journal of chemical physics, 2004-06, Vol.120 (24), p.11919-11929

2004

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CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

Proceedings of the National Academy of Sciences - PNAS, 2017-07, Vol.114 (28), p.7260-7265

2017

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Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins

Chemical reviews, 2006-05, Vol.106 (5), p.1589-1615

2006

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Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics

The journal of physical chemistry letters, 2023-11, Vol.14 (44), p.9926-9934

2023

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Water in Cavity−Ligand Recognition

Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor

Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

Molecular dynamics simulations and drug discovery

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

A glycan gate controls opening of the SARS-CoV-2 spike protein

G-protein coupled receptors: advances in simulation and drug discovery

Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV‑2 Main Protease

Molecular recognition and ligand association

NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function

Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations

Ensemble Docking in Drug Discovery

Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor

Improvements to the APBS biomolecular solvation software suite

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

Membrane Allostery and Unique Hydrophobic Sites Promote Enzyme Substrate Specificity

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

Accelerated molecular dynamics simulations of protein folding

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins

Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics

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