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Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

Journal of chemical information and modeling, 2016-04, Vol.56 (4), p.721-733

2016

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Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?

Chemical biology & drug design, 2013-01, Vol.81 (1), p.61-71

2013

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Mechanism of 150-cavity formation in influenza neuraminidase

Nature communications, 2011-07, Vol.2 (1), p.388-388, Article 388

2011

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Rational prediction with molecular dynamics for hit identification

Current topics in medicinal chemistry, 2012-09, Vol.12 (18), p.2002-2012

2012

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Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1

PLoS neglected tropical diseases, 2010-08, Vol.4 (8), p.e803-e803

2010

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Modeling the pharmacodynamics of passive membrane permeability

Journal of computer-aided molecular design, 2011-11, Vol.25 (11), p.1007-1017

2011

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Substrate Induced Population Shifts and Stochastic Gating in the PBCV-1 mRNA Capping Enzyme

Journal of the American Chemical Society, 2009-04, Vol.131 (14), p.5126-5133

2009

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Computation-Guided Discovery of Influenza Endonuclease Inhibitors

ACS medicinal chemistry letters, 2014-01, Vol.5 (1), p.61-64

2014

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Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking

Structure (London), 2019-08, Vol.27 (8), p.1326-1335.e4

2019

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Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis

PloS one, 2011-09, Vol.6 (9), p.e25084-e25084

2011

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Catalytically Requisite Conformational Dynamics in the mRNA-Capping Enzyme Probed by Targeted Molecular Dynamics

Biochemistry (Easton), 2008-04, Vol.47 (13), p.4102-4111

2008

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Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations

Journal of chemical information and modeling, 2016-10, Vol.56 (10), p.1923-1935

2016

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Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles

Journal of chemical information and modeling, 2016-05, Vol.56 (5), p.830-842

2016

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Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei

PLoS neglected tropical diseases, 2007-11, Vol.1 (2), p.e68

2007

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Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics

Journal of computational chemistry, 2009-08, Vol.30 (11), p.1719-1725

2009

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Molecular docking to flexible targets

Methods in molecular biology (Clifton, N.J.), 2015, Vol.1215, p.445

2015

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Magnesium-Induced Nucleophile Activation in the Guanylyltransferase mRNA Capping Enzyme

Biochemistry (Easton), 2012-12, Vol.51 (51), p.10236-10243

2012

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Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms

Expert opinion on drug discovery, 2009-12, Vol.4 (12), p.1281-1294

2009

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Toward Understanding the Conformational Dynamics of RNA Ligation

Biochemistry (Easton), 2009-02, Vol.48 (4), p.709-719

2009

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Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations

Procedia computer science, 2014, Vol.29, p.1745-1755

2014

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Myxopyronin induced bacterial RNA polymerase dynamics and computer aided drug discovery

The FASEB journal, 2010-04, Vol.24 (S1), p.752.7-752.7

2010

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Rational Prediction with Molecular Dynamics for Hit Identification

Current topics in medicinal chemistry, 2013-01, Vol.12 (18), p.2002-2012

2013

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Catalytically Requisite Conformational Dynamics in the mRNA-Capping Enzyme Probed by Targeted Molecular Dynamics super([dagger])

Biochemistry (Easton), 2008-01, Vol.47 (13), p.4102-4111

2008

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Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase

Journal of molecular and genetic medicine, 2012, Vol.6 (1), p.293-300

2012

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Chapter 12 - Molecular Simulation in Computer-aided Drug Design: Algorithms and Applications

Innovations in Biomolecular Modeling and Simulations: Volume 2, 2012, Vol.2, p.281-315

2012

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Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?

Mechanism of 150-cavity formation in influenza neuraminidase

Rational prediction with molecular dynamics for hit identification

Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1

Modeling the pharmacodynamics of passive membrane permeability

Substrate Induced Population Shifts and Stochastic Gating in the PBCV-1 mRNA Capping Enzyme

Computation-Guided Discovery of Influenza Endonuclease Inhibitors

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking

Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis

Catalytically Requisite Conformational Dynamics in the mRNA-Capping Enzyme Probed by Targeted Molecular Dynamics

Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations

Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles

Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics

Molecular docking to flexible targets

Magnesium-Induced Nucleophile Activation in the Guanylyltransferase mRNA Capping Enzyme

Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms

Toward Understanding the Conformational Dynamics of RNA Ligation

Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations

Myxopyronin induced bacterial RNA polymerase dynamics and computer aided drug discovery

Rational Prediction with Molecular Dynamics for Hit Identification

Catalytically Requisite Conformational Dynamics in the mRNA-Capping Enzyme Probed by Targeted Molecular Dynamics super([dagger])

Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase

Chapter 12 - Molecular Simulation in Computer-aided Drug Design: Algorithms and Applications

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