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Improving Small Molecule pKa Prediction Using Transfer Learning With Graph Neural Networks

Frontiers in chemistry, 2022-05, Vol.10

2022

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Improved Lipophilicity and Aqueous Solubility Prediction with Composite Graph Neural Networks

Molecules (Basel, Switzerland), 2021-10, Vol.26 (20), p.6185

2021

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Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations

Journal of chemical information and modeling, 2017-02, Vol.57 (2), p.365-385

2017

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Protex-A Python utility for proton exchange in molecular dynamics simulations

Frontiers in chemistry, 2023-02, Vol.11, p.1140896

2023

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Discovery of Potent Inhibitors for the Large Neutral Amino Acid Transporter 1 (LAT1) by Structure-Based Methods

International journal of molecular sciences, 2018-12, Vol.20 (1), p.27

2018

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Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool

Frontiers in molecular biosciences, 2022-09, Vol.9, p.954638-954638

2022

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Dummy Atoms in Alchemical Free Energy Calculations

Journal of chemical theory and computation, 2021-07, Vol.17 (7), p.4403-4419

2021

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Computational Identification of Novel Kir6 Channel Inhibitors

Frontiers in pharmacology, 2019-05, Vol.10, p.549

2019

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Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution

Chemical science (Cambridge), 2021-09, Vol.12 (34), p.11364-11381

2021

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Calculations of Absolute Solvation Free Energies with TransformatoApplication to the FreeSolv Database Using the CGenFF Force Field

Journal of chemical theory and computation, 2023-09, Vol.19 (17), p.5988-5998

2023

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Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program

Journal of computational chemistry, 2022-06, Vol.43 (17), p.1151-1160

2022

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Improving Small Molecule pK a Prediction Using Transfer Learning With Graph Neural Networks

Frontiers in chemistry, 2022-05, Vol.10, p.866585-866585

2022

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Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential

The journal of physical chemistry. B, 2024-07, Vol.128 (28), p.6693-6703

2024

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Reweighting from Molecular Mechanics Force Fields to the ANI-2x Neural Network Potential

Journal of chemical theory and computation, 2024-04, Vol.20 (7), p.2719-2728

2024

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A Molecular Dynamics–Shared Pharmacophore Approach to Boost Early‐Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator‐Activated Receptor α

ChemMedChem, 2017-08, Vol.12 (16), p.1399-1407

2017

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Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations

Monatshefte für Chemie, 2016, Vol.147 (3), p.553-563

2016

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Evaluating the stability of pharmacophore features using molecular dynamics simulations

Biochemical and biophysical research communications, 2016-02, Vol.470 (3), p.685-689

2016

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Structure–Activity Relationships of Novel Thiazole-Based Modafinil Analogues Acting at Monoamine Transporters

Journal of medicinal chemistry, 2020-01, Vol.63 (1), p.391-417

2020

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A daily single dose of a novel modafinil analogue CE-123 improves memory acquisition and memory retrieval

Behavioural brain research, 2018-05, Vol.343, p.83-94

2018

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Heterocyclic Analogues of Modafinil as Novel, Atypical Dopamine Transporter Inhibitors

Journal of medicinal chemistry, 2017-11, Vol.60 (22), p.9330-9348

2017

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POLθ processes ssDNA gaps and promotes replication fork progression in BRCA1-deficient cells

Cell reports (Cambridge), 2022-11, Vol.41 (9), p.111716-111716, Article 111716

2022

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SAR-Guided Scoring Function and Mutational Validation Reveal the Binding Mode of CGS-8216 at the a1+/?2– Benzodiazepine Site

Journal of chemical information and modeling, 2018-08, Vol.58 (8), p.1682

2018

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Pharmacophore Models Derived from Molecular Dynamics Simulations of Protein-Ligand Complexes: A Case Study

Natural product communications, 2016-10, Vol.11 (10), p.1499-1504

2016

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A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Receptor[alpha]

ChemMedChem, 2017-08, Vol.12 (16), p.1399

2017

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Synthesis and dopamine receptor binding of dihydrexidine and SKF 38393 catecholamine-based analogues

Amino acids, 2022, Vol.54 (1), p.85-98

2022

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Improving Small Molecule pKa Prediction Using Transfer Learning With Graph Neural Networks

Improved Lipophilicity and Aqueous Solubility Prediction with Composite Graph Neural Networks

Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations

Protex-A Python utility for proton exchange in molecular dynamics simulations

Discovery of Potent Inhibitors for the Large Neutral Amino Acid Transporter 1 (LAT1) by Structure-Based Methods

Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool

Dummy Atoms in Alchemical Free Energy Calculations

Computational Identification of Novel Kir6 Channel Inhibitors

Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution

Calculations of Absolute Solvation Free Energies with TransformatoApplication to the FreeSolv Database Using the CGenFF Force Field

Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program

Improving Small Molecule pK a Prediction Using Transfer Learning With Graph Neural Networks

Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential

Reweighting from Molecular Mechanics Force Fields to the ANI-2x Neural Network Potential

A Molecular Dynamics–Shared Pharmacophore Approach to Boost Early‐Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator‐Activated Receptor α

Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations

Evaluating the stability of pharmacophore features using molecular dynamics simulations

Structure–Activity Relationships of Novel Thiazole-Based Modafinil Analogues Acting at Monoamine Transporters

A daily single dose of a novel modafinil analogue CE-123 improves memory acquisition and memory retrieval

Heterocyclic Analogues of Modafinil as Novel, Atypical Dopamine Transporter Inhibitors

POLθ processes ssDNA gaps and promotes replication fork progression in BRCA1-deficient cells

SAR-Guided Scoring Function and Mutational Validation Reveal the Binding Mode of CGS-8216 at the a1+/?2– Benzodiazepine Site

Pharmacophore Models Derived from Molecular Dynamics Simulations of Protein-Ligand Complexes: A Case Study

A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Receptor[alpha]

Synthesis and dopamine receptor binding of dihydrexidine and SKF 38393 catecholamine-based analogues

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