Prediction of Ligand Binding Affinity and Orientation of Xenoestrogens to the Estrogen Receptor by Molecular Dynamics Simulations and the Linear Interaction Energy Method

Marola M. H. van Lipzig; Antonius M. ter Laak; Aldo Jongejan; Nico P. E. Vermeulen; Mirjam Wamelink; Daan Geerke; John. H. N. Meerman

doi:10.1021/jm0309607

Prediction of Ligand Binding Affinity and Orientation of Xenoestrogens to the Estrogen Receptor by Molecular Dynamics Simulations and the Linear Interaction Energy Method

Journal of Medicinal Chemistry ◽

10.1021/jm0309607 ◽

2004 ◽

Vol 47 (4) ◽

pp. 1018-1030 ◽

Cited By ~ 61

Author(s):

Marola M. H. van Lipzig ◽

Antonius M. ter Laak ◽

Aldo Jongejan ◽

Nico P. E. Vermeulen ◽

Mirjam Wamelink ◽

...

Keyword(s):

Molecular Dynamics ◽

Estrogen Receptor ◽

Ligand Binding ◽

Molecular Dynamics Simulations ◽

Interaction Energy ◽

Binding Affinity ◽

Energy Method ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Dynamics Simulations

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What determines the van der Waals coefficient ? in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?

Proteins Structure Function and Bioinformatics ◽

10.1002/(sici)1097-0134(19990215)34:3<395::aid-prot11>3.0.co;2-4 ◽

1999 ◽

Vol 34 (3) ◽

pp. 395-402 ◽

Cited By ~ 82

Author(s):

Wei Wang ◽

Jian Wang ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Interaction Energy ◽

Energy Method ◽

Van Der Waals ◽

Free Energies ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Dynamics Simulations ◽

Binding Free Energies

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Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods

Computational and Structural Biotechnology Journal ◽

10.1016/j.csbj.2020.02.007 ◽

2020 ◽

Vol 18 ◽

pp. 439-454 ◽

Cited By ~ 3

Author(s):

Debby D. Wang ◽

Le Ou-Yang ◽

Haoran Xie ◽

Mengxu Zhu ◽

Hong Yan

Keyword(s):

Machine Learning ◽

Molecular Dynamics ◽

Ligand Binding ◽

Molecular Dynamics Simulations ◽

Binding Affinity ◽

Learning Methods ◽

Machine Learning Methods ◽

Dynamics Simulations

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Binding affinity models for Falcipain inhibition based on the Linear Interaction Energy method

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2016.06.008 ◽

2016 ◽

Vol 70 ◽

pp. 236-245 ◽

Cited By ~ 3

Author(s):

Vasanthanathan Poongavanam ◽

Jacob Kongsted

Keyword(s):

Interaction Energy ◽

Binding Affinity ◽

Energy Method ◽

Linear Interaction ◽

Linear Interaction Energy

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Calculation of the Binding Affinity of β-Secretase Inhibitors Using the Linear Interaction Energy Method

Journal of Medicinal Chemistry ◽

10.1021/jm020513b ◽

2003 ◽

Vol 46 (11) ◽

pp. 2074-2082 ◽

Cited By ~ 37

Author(s):

Brett A. Tounge ◽

Charles H. Reynolds

Keyword(s):

Interaction Energy ◽

Binding Affinity ◽

Energy Method ◽

Linear Interaction ◽

Linear Interaction Energy

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Applying linear interaction energy method for binding affinity calculations of podophyllotoxin analogues with tubulin using continuum solvent model and prediction of cytotoxic activity

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2009.02.003 ◽

2009 ◽

Vol 27 (8) ◽

pp. 930-943 ◽

Cited By ~ 14

Author(s):

Md. Afroz Alam ◽

Pradeep Kumar Naik

Keyword(s):

Cytotoxic Activity ◽

Interaction Energy ◽

Binding Affinity ◽

Energy Method ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Continuum Solvent Model ◽

Solvent Model ◽

Binding Affinity Calculations

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Combining Docking, Molecular Dynamics and the Linear Interaction Energy Method to Predict Binding Modes and Affinities for Non-nucleoside Inhibitors to HIV-1 Reverse Transcriptase

Journal of Medicinal Chemistry ◽

10.1021/jm7012198 ◽

2008 ◽

Vol 51 (9) ◽

pp. 2648-2656 ◽

Cited By ~ 59

Author(s):

Jens Carlsson ◽

Lars Boukharta ◽

Johan Åqvist

Keyword(s):

Molecular Dynamics ◽

Reverse Transcriptase ◽

Interaction Energy ◽

Energy Method ◽

Binding Modes ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Nucleoside Inhibitors ◽

Hiv 1

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The Linear Interaction Energy Method for Predicting Ligand Binding Free Energies

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207013330661 ◽

2001 ◽

Vol 4 (8) ◽

pp. 613-626 ◽

Cited By ~ 101

Author(s):

Johan Aqvist ◽

John Marelius

Keyword(s):

Ligand Binding ◽

Interaction Energy ◽

Energy Method ◽

Free Energies ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Binding Free Energies

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Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method

Journal of Chemical Information and Modeling ◽

10.1021/ci0601214 ◽

2006 ◽

Vol 46 (5) ◽

pp. 1972-1983 ◽

Cited By ~ 42

Author(s):

Eva Stjernschantz ◽

John Marelius ◽

Carmen Medina ◽

Micael Jacobsson ◽

Nico P. E. Vermeulen ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Interaction Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Linear Interaction ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations

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Binding affinity prediction with different force fields: Examination of the linear interaction energy method

Journal of Computational Chemistry ◽

10.1002/jcc.20047 ◽

2004 ◽

Vol 25 (10) ◽

pp. 1242-1254 ◽

Cited By ~ 85

Author(s):

Martin Almlöf ◽

BjØrn O. Brandsdal ◽

Johan Åqvist

Keyword(s):

Interaction Energy ◽

Binding Affinity ◽

Energy Method ◽

Force Fields ◽

Linear Interaction ◽

Binding Affinity Prediction ◽

Linear Interaction Energy ◽

Affinity Prediction

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Calculate protein–ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-018-0162-6 ◽

2018 ◽

Vol 33 (1) ◽

pp. 105-117 ◽

Cited By ~ 12

Author(s):

Xibing He ◽

Viet H. Man ◽

Beihong Ji ◽

Xiang-Qun Xie ◽

Junmei Wang

Keyword(s):

Ligand Binding ◽

Interaction Energy ◽

Energy Method ◽

Cathepsin S ◽

Grand Challenge ◽

Binding Affinities ◽

Linear Interaction ◽

Linear Interaction Energy

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