Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent:  Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase

Yang Su; Emilio Gallicchio; Kalyan Das; Eddy Arnold; Ronald M. Levy

doi:10.1021/ct600258e

Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase

Journal of Chemical Theory and Computation ◽

10.1021/ct600258e ◽

2006 ◽

Vol 3 (1) ◽

pp. 256-277 ◽

Cited By ~ 34

Author(s):

Yang Su ◽

Emilio Gallicchio ◽

Kalyan Das ◽

Eddy Arnold ◽

Ronald M. Levy

Keyword(s):

Ligand Binding ◽

Reverse Transcriptase ◽

Interaction Energy ◽

Implicit Solvent ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Hiv 1

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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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Linear interaction energy approximation for binding affinities of nevirapine and HEPT analogues with HIV-1 reverse transcriptase

Molecular Simulation ◽

10.1080/08927020902929828 ◽

2009 ◽

Vol 35 (15) ◽

pp. 1224-1241 ◽

Cited By ~ 4

Author(s):

Antonios Tavlarakis ◽

Ruhong Zhou

Keyword(s):

Reverse Transcriptase ◽

Interaction Energy ◽

Binding Affinities ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Energy Approximation ◽

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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Calculation of binding affinities of HIV-1 RT and β-secretase inhibitors using the linear interaction energy method with explicit and continuum solvation approaches

Journal of Molecular Modeling ◽

10.1007/s00894-007-0229-0 ◽

2007 ◽

Vol 13 (10) ◽

pp. 1081-1097 ◽

Cited By ~ 5

Author(s):

Niall J. English

Keyword(s):

Interaction Energy ◽

Energy Method ◽

Binding Affinities ◽

Continuum Solvation ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Hiv 1

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Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein–Ligand Binding Geometry and Free Energy

Journal of Chemical Information and Modeling ◽

10.1021/ci1003009 ◽

2011 ◽

Vol 51 (9) ◽

pp. 2047-2065 ◽

Cited By ~ 19

Author(s):

Obaidur Rahaman ◽

Trilce P. Estrada ◽

Douglas J. Doren ◽

Michela Taufer ◽

Charles L. Brooks ◽

...

Keyword(s):

Free Energy ◽

Ligand Binding ◽

Interaction Energy ◽

Scoring Functions ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Pair Potentials

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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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A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1–Ligand Binding Free Energy Calculation

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.9b00609 ◽

2019 ◽

Vol 59 (9) ◽

pp. 4018-4033 ◽

Cited By ~ 5

Author(s):

Eko Aditya Rifai ◽

Marc van Dijk ◽

Nico P. E. Vermeulen ◽

Arry Yanuar ◽

Daan P. Geerke

Keyword(s):

Free Energy ◽

Ligand Binding ◽

Interaction Energy ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Binding Free Energy Calculation

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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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Linear interaction energy models for β-secretase (BACE) inhibitors: Role of van der Waals, electrostatic, and continuum-solvation terms

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2005.10.002 ◽

2006 ◽

Vol 24 (6) ◽

pp. 475-484 ◽

Cited By ~ 19

Author(s):

Brett A. Tounge ◽

Ramkumar Rajamani ◽

Ellen W. Baxter ◽

Allen B. Reitz ◽

Charles H. Reynolds

Keyword(s):

Interaction Energy ◽

Van Der Waals ◽

Continuum Solvation ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Energy Models

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In Silico Binding Free Energy Predictability by Using the Linear Interaction Energy (LIE) Method: Bromobenzimidazole CK2 Inhibitors as a Case Study

Journal of Chemical Information and Modeling ◽

10.1021/ci600369n ◽

2007 ◽

Vol 47 (2) ◽

pp. 572-582 ◽

Cited By ~ 24

Author(s):

A. Bortolato ◽

S. Moro

Keyword(s):

Free Energy ◽

Interaction Energy ◽

In Silico ◽

Binding Free Energy ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Ck2 Inhibitors

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