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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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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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Effects of somatic mutations on CDR loop flexibility during affinity maturation

Proteins, structure, function, and bioinformatics, 2011-03, Vol.79 (3), p.821-829

2011

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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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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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Strengths of Hydrogen Bonds Involving Phosphorylated Amino Acid Side Chains

Journal of the American Chemical Society, 2007-01, Vol.129 (4), p.820-827

2007

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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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Hot-spot residues at the E9/Im9 interface help binding via different mechanisms

Biopolymers, 2008-11, Vol.89 (11), p.916-920

2008

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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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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

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

Effects of somatic mutations on CDR loop flexibility during affinity maturation

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

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

Tricyclic GyrB/ParE (TriBE) inhibitors: a new class of broad-spectrum dual-targeting antibacterial agents

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

Strengths of Hydrogen Bonds Involving Phosphorylated Amino Acid Side Chains

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

Hot-spot residues at the E9/Im9 interface help binding via different mechanisms

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

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