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A Method to Predict Blood-Brain Barrier Permeability of Drug-Like Compounds Using Molecular Dynamics Simulations

Biophysical journal, 2014-08, Vol.107 (3), p.630-641

2014

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Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines

PloS one, 2014-09, Vol.9 (9), p.e106298

2014

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Understanding a substrate's product regioselectivity in a family of enzymes: a case study of acetaminophen binding in cytochrome P450s

PloS one, 2014-02, Vol.9 (2), p.e87058-e87058

2014

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Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference

Journal of chemical information and modeling, 2021-04, Vol.61 (4), p.1583-1592

2021

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Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap

Expert opinion on drug discovery, 2013-03, Vol.8 (3), p.277-287

2013

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Rapid catalytic template searching as an enzyme function prediction procedure

PloS one, 2013-05, Vol.8 (5), p.e62535-e62535

2013

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Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment

Journal of chemical information and modeling, 2014-01, Vol.54 (1), p.324-337

2014

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Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

Journal of computational chemistry, 2013-04, Vol.34 (11), p.915-927

2013

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Comparison and analysis of zinc and cobalt-based systems as catalytic entities for the hydration of carbon dioxide

PloS one, 2013-06, Vol.8 (6), p.e66187-e66187

2013

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Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method

Journal of chemical information and modeling, 2023-11, Vol.63 (21), p.6655-6666

2023

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Accounting for water molecules in drug design

Expert opinion on drug discovery, 2011-01, Vol.6 (1), p.65-74

2011

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Toward a Small Molecule, Biomimetic Carbonic Anhydrase Model: Theoretical and Experimental Investigations of a Panel of Zinc(II) Aza-Macrocyclic Catalysts

Inorganic chemistry, 2012-06, Vol.51 (12), p.6803-6812

2012

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Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity

Bioorganic & medicinal chemistry letters, 2013-03, Vol.23 (5), p.1529-1536

2013

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Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE), Part II: Development of inhibitors with broad spectrum, Gram-negative antibacterial activity

Bioorganic & medicinal chemistry letters, 2013-03, Vol.23 (5), p.1537-1543

2013

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Molecular Recognition of Aromatic Rings by Flavin: Electrostatics and Dispersion Determine Ring Positioning above Isoalloxazine

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2013-12, Vol.117 (48), p.12946-12952

2013

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Competition between Intramolecular Hydrogen Bonds and Solvation in Phosphorylated Peptides: Simulations with Explicit and Implicit Solvent

The journal of physical chemistry. B, 2005-03, Vol.109 (11), p.5249-5258

2005

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Efficient Computational Modeling of Human Ventricular Activation and Its Electrocardiographic Representation: A Sensitivity Study

Cardiovascular engineering and technology, 2018-09, Vol.9 (3), p.447-467

2018

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Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics

Journal of chemical theory and computation, 2013-03, Vol.9 (3), p.1320-1327

2013

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Developing an approach for first‐principles catalyst design: application to carbon‐capture catalysis

Acta crystallographica. Section C, Crystal structure communications, 2014-02, Vol.70 (2), p.123-131

2014

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E9-Im9 Colicin DNase−Immunity Protein Biomolecular Association in Water: A Multiple-Copy and Accelerated Molecular Dynamics Simulation Study

The journal of physical chemistry. B, 2008-12, Vol.112 (51), p.16802-16814

2008

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Methyl Motional Parameters in Crystalline l-Alanine: Molecular Dynamics Simulation and NMR

The journal of physical chemistry. B, 2000-11, Vol.104 (47), p.11342-11348

2000

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Methyl dynamics in crystalline amino acids: MD and NMR

Journal of computational chemistry, 2003-07, Vol.24 (9), p.1052-1058

2003

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Leveraging structural information for the discovery of new drugs: computational methods

Methods in molecular biology (Clifton, N.J.), 2012, Vol.841, p.209

2012

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Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap [WaterMap and Its Implementation in Drug Discovery]

Expert opinion on drug discovery, 2012-09, Vol.8 (3)

2012

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Understanding a Substrate's Product Regioselectivity in a Family of Enzymes: A Case Study of Acetaminophen Binding in Cytochrome P450s: e87058

PloS one, 2014-02, Vol.9 (2)

2014

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A Method to Predict Blood-Brain Barrier Permeability of Drug-Like Compounds Using Molecular Dynamics Simulations

Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines

Understanding a substrate's product regioselectivity in a family of enzymes: a case study of acetaminophen binding in cytochrome P450s

Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference

Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap

Rapid catalytic template searching as an enzyme function prediction procedure

Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment

Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

Comparison and analysis of zinc and cobalt-based systems as catalytic entities for the hydration of carbon dioxide

Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method

Accounting for water molecules in drug design

Toward a Small Molecule, Biomimetic Carbonic Anhydrase Model: Theoretical and Experimental Investigations of a Panel of Zinc(II) Aza-Macrocyclic Catalysts

Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity

Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE), Part II: Development of inhibitors with broad spectrum, Gram-negative antibacterial activity

Molecular Recognition of Aromatic Rings by Flavin: Electrostatics and Dispersion Determine Ring Positioning above Isoalloxazine

Competition between Intramolecular Hydrogen Bonds and Solvation in Phosphorylated Peptides: Simulations with Explicit and Implicit Solvent

Efficient Computational Modeling of Human Ventricular Activation and Its Electrocardiographic Representation: A Sensitivity Study

Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics

Developing an approach for first‐principles catalyst design: application to carbon‐capture catalysis

E9-Im9 Colicin DNase−Immunity Protein Biomolecular Association in Water: A Multiple-Copy and Accelerated Molecular Dynamics Simulation Study

Methyl Motional Parameters in Crystalline l-Alanine: Molecular Dynamics Simulation and NMR

Methyl dynamics in crystalline amino acids: MD and NMR

Leveraging structural information for the discovery of new drugs: computational methods

Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap [WaterMap and Its Implementation in Drug Discovery]

Understanding a Substrate's Product Regioselectivity in a Family of Enzymes: A Case Study of Acetaminophen Binding in Cytochrome P450s: e87058

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