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Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening

PloS one, 2019-08, Vol.14 (8), p.e0220113

2019

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Lipid21: Complex Lipid Membrane Simulations with AMBER

Journal of chemical theory and computation, 2022-03, Vol.18 (3), p.1726-1736

2022

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Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

Journal of the American Chemical Society, 2017-01, Vol.139 (1), p.442-452

2017

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Revealing Molecular Determinants of hERG Blocker and Activator Binding

Journal of chemical information and modeling, 2020-01, Vol.60 (1), p.192-203

2020

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Lipid14: The Amber Lipid Force Field

Journal of chemical theory and computation, 2014-02, Vol.10 (2), p.865-879

2014

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GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Soft matter, 2012-01, Vol.8 (37), p.9617-9627

2012

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Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules

Journal of chemical information and modeling, 2019-01, Vol.59 (1), p.236-244

2019

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Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots

Journal of chemical information and modeling, 2021-12, Vol.61 (12), p.5923-5930

2021

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Leveraging Advanced In Silico Techniques in Early Drug Discovery: A Study of Potent Small-Molecule YAP-TEAD PPI Disruptors

Journal of chemical information and modeling, 2023-04, Vol.63 (8), p.2520-2531

2023

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Calculating Kinetic Rates and Membrane Permeability from Biased Simulations

The journal of physical chemistry. B, 2018-12, Vol.122 (49), p.11571-11578

2018

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Contributions of the membrane dipole potential to the function of voltage-gated cation channels and modulation by small molecule potentiators

Biochimica et biophysica acta. Biomembranes, 2017-02, Vol.1859 (2), p.177-194

2017

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Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

Chemical science (Cambridge), 2021-01, Vol.12 (4), p.1513-1527

2021

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Scorpion α-toxin LqhαIT specifically interacts with a glycan at the pore domain of voltage-gated sodium channels

Structure (London), 2024-10, Vol.32 (10), p.1611-1620.e4

2024

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Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics

Journal of chemical theory and computation, 2022-04, Vol.18 (4), p.2543-2555

2022

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Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design

Journal of computer-aided molecular design, 2024-12, Vol.38 (1), p.21-21, Article 21

2024

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Imaging phase separation in model lipid membranes through the use of BODIPY based molecular rotors

Physical chemistry chemical physics : PCCP, 2015-07, Vol.17 (28), p.18393-18402

2015

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All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields

Chemical communications (Cambridge, England), 2015-03, Vol.51 (21), p.4402-4405

2015

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Simulation of lipid bilayer self-assembly using all-atom lipid force fields

Physical chemistry chemical physics : PCCP, 2016-04, Vol.18 (15), p.10573-10584

2016

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Imaging plasma membrane phase behaviour in live cells using a thiophene-based molecular rotor

Chemical communications (Cambridge, England), 2016-01, Vol.52 (90), p.13269-13272

2016

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Uncoupling the Structure–Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding

Journal of medicinal chemistry, 2016-06, Vol.59 (12), p.5780-5789

2016

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Building New Bridges between In Vitro and In Vivo in Early Drug Discovery: Where Molecular Modeling Meets Systems Biology

Current topics in medicinal chemistry, 2017-01, Vol.17 (23), p.2642

2017

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Further evaluation of quantum chemical methods for the prediction of non-specific binding of positron emission tomography tracers

Physical chemistry chemical physics : PCCP, 2011-01, Vol.13 (48), p.21552-21557

2011

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Chalcogen OCF3 Isosteres Modulate Drug Properties without Introducing Inherent Liabilities

ChemMedChem, 2019-09, Vol.14 (17), p.1586-1589

2019

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Chalcogen OCF 3 Isosteres Modulate Drug Properties without Introducing Inherent Liabilities

ChemMedChem, 2019-09, Vol.14 (17), p.1586-1589

2019

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Simulation of lipid bilayer self-assembly using all-atom lipid force fieldsElectronic supplementary information (ESI) available. See DOI: 10.1039/c5cp07379k

2016-04

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Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening

Lipid21: Complex Lipid Membrane Simulations with AMBER

Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

Revealing Molecular Determinants of hERG Blocker and Activator Binding

Lipid14: The Amber Lipid Force Field

GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules

Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots

Leveraging Advanced In Silico Techniques in Early Drug Discovery: A Study of Potent Small-Molecule YAP-TEAD PPI Disruptors

Calculating Kinetic Rates and Membrane Permeability from Biased Simulations

Contributions of the membrane dipole potential to the function of voltage-gated cation channels and modulation by small molecule potentiators

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

Scorpion α-toxin LqhαIT specifically interacts with a glycan at the pore domain of voltage-gated sodium channels

Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics

Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design

Imaging phase separation in model lipid membranes through the use of BODIPY based molecular rotors

All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields

Simulation of lipid bilayer self-assembly using all-atom lipid force fields

Imaging plasma membrane phase behaviour in live cells using a thiophene-based molecular rotor

Uncoupling the Structure–Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding

Building New Bridges between In Vitro and In Vivo in Early Drug Discovery: Where Molecular Modeling Meets Systems Biology

Further evaluation of quantum chemical methods for the prediction of non-specific binding of positron emission tomography tracers

Chalcogen OCF3 Isosteres Modulate Drug Properties without Introducing Inherent Liabilities

Chalcogen OCF 3 Isosteres Modulate Drug Properties without Introducing Inherent Liabilities

Simulation of lipid bilayer self-assembly using all-atom lipid force fieldsElectronic supplementary information (ESI) available. See DOI: 10.1039/c5cp07379k

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