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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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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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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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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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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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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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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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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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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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Recent advances on structure-informed drug discovery of cyclin-dependent kinase-2 inhibitors

Future medicinal chemistry, 2009-11, Vol.1 (8), p.1453-1466

Duca, José S

2009

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Noticing the unnoticed: bridging structural data and drug design

Future medicinal chemistry, 2012-10, Vol.4 (15), p.1869-1871

2012

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Cross-Docking of Inhibitors into CDK2 Structures. 1

Journal of chemical information and modeling, 2008-03, Vol.48 (3), p.659-668

2008

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soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts

Nucleic acids research, 2008-07, Vol.36 (Web Server issue), p.W252-W254

2008

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Cross-Docking of Inhibitors into CDK2 Structures. 2

Journal of chemical information and modeling, 2008-03, Vol.48 (3), p.669-678

2008

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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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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 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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Insights from ab initio quantum chemical calculations into the preferred tautomeric forms and binding affinities to CDK2 of substituted pyrazolopyridines

Biopolymers, 2005, Vol.80 (2-3), p.312-318

2005

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

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

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

Quantum mechanical approaches to structurally informed design

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

Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

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

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

Revealing Molecular Determinants of hERG Blocker and Activator Binding

Recent advances on structure-informed drug discovery of cyclin-dependent kinase-2 inhibitors

Noticing the unnoticed: bridging structural data and drug design

Cross-Docking of Inhibitors into CDK2 Structures. 1

soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts

Cross-Docking of Inhibitors into CDK2 Structures. 2

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

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

Insights from ab initio quantum chemical calculations into the preferred tautomeric forms and binding affinities to CDK2 of substituted pyrazolopyridines

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

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

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