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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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Rethinking drug design in the artificial intelligence era

Nature reviews. Drug discovery, 2020-05, Vol.19 (5), p.353-364

2020

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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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Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K‑Ras4B Dimer Stability

The journal of physical chemistry. B, 2022-02, Vol.126 (7), p.1504-1519

2022

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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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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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Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen–Hydrogen Correlations

Journal of chemical theory and computation, 2015-11, Vol.11 (11), p.5090-5102

2015

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Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications

Journal of chemical theory and computation, 2023-12, Vol.19 (23), p.8901-8918

2023

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Implications of Dynamic Occupancy, Binding Kinetics, and Channel Gating Kinetics for hERG Blocker Safety Assessment and Mitigation

Current topics in medicinal chemistry, 2016-07, Vol.16 (16), p.1792-1818

2016

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LMX1B Mutations Cause Hereditary FSGS without Extrarenal Involvement

Journal of the American Society of Nephrology, 2013-07, Vol.24 (8), p.1216-1222

2013

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Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

Journal of chemical theory and computation, 2021-05, Vol.17 (5), p.3088-3102

2021

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Structure-guided discovery of cyclin-dependent kinase inhibitors

Biopolymers, 2008-05, Vol.89 (5), p.372-379

2008

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Structure-based design and optimization of 2-aminothiazole-4-carboxamide as a new class of CHK1 inhibitors

Bioorganic & medicinal chemistry letters, 2013-05, Vol.23 (9), p.2590-2594

2013

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Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: A template-based approach—Part 1

Bioorganic & medicinal chemistry letters, 2011-01, Vol.21 (1), p.467-470

2011

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Discovery of a Novel Series of CHK1 Kinase Inhibitors with a Distinctive Hinge Binding Mode

ACS medicinal chemistry letters, 2012-02, Vol.3 (2), p.123-128

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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Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: A template-based approach—Part 2

Bioorganic & medicinal chemistry letters, 2011-01, Vol.21 (1), p.471-474

2011

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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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Thermodynamics of Nucleotide and Inhibitor Binding to Wild-Type and Ispinesib-Resistant Forms of Human Kinesin Spindle Protein

Biochemistry (Easton), 2009-11, Vol.48 (46), p.11045-11055

2009

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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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Inhibitors of hepatitis C virus polymerase: Synthesis and characterization of novel 2-oxy-6-fluoro- N-(( S)-1-hydroxy-3-phenylpropan-2-yl)-benzamides

Bioorganic & medicinal chemistry letters, 2010-04, Vol.20 (7), p.2119-2124

2010

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Time-Averaged Distributions of Solute and Solvent Motions: Exploring Proton Wires of GFP and PfM2DH

Journal of chemical information and modeling, 2014-12, Vol.54 (12), p.3344-3361

2014

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Collaborating to improve the use of free-energy and other quantitative methods in drug discovery

Journal of computer-aided molecular design, 2016-12, Vol.30 (12), p.1139-1141

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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Quantum mechanical approaches to structurally informed design

International journal of quantum chemistry, 2014-03, Vol.114 (5), p.305-313

2014

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

Rethinking drug design in the artificial intelligence era

Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K‑Ras4B Dimer Stability

Revealing Molecular Determinants of hERG Blocker and Activator Binding

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

Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen–Hydrogen Correlations

Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications

Implications of Dynamic Occupancy, Binding Kinetics, and Channel Gating Kinetics for hERG Blocker Safety Assessment and Mitigation

LMX1B Mutations Cause Hereditary FSGS without Extrarenal Involvement

Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

Structure-guided discovery of cyclin-dependent kinase inhibitors

Structure-based design and optimization of 2-aminothiazole-4-carboxamide as a new class of CHK1 inhibitors

Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: A template-based approach—Part 1

Discovery of a Novel Series of CHK1 Kinase Inhibitors with a Distinctive Hinge Binding Mode

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

Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: A template-based approach—Part 2

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

Thermodynamics of Nucleotide and Inhibitor Binding to Wild-Type and Ispinesib-Resistant Forms of Human Kinesin Spindle Protein

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

Inhibitors of hepatitis C virus polymerase: Synthesis and characterization of novel 2-oxy-6-fluoro- N-(( S)-1-hydroxy-3-phenylpropan-2-yl)-benzamides

Time-Averaged Distributions of Solute and Solvent Motions: Exploring Proton Wires of GFP and PfM2DH

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery

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

Quantum mechanical approaches to structurally informed design

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