Estimation of the Binding Free Energy by Linear Interaction Energy Models

Mini-Reviews in Medicinal Chemistry ◽

10.2174/138955712800493843 ◽

2012 ◽

Vol 12 (6) ◽

pp. 551-561 ◽

Author(s):

O. Nicolotti ◽

M. Convertino ◽

F. Leonetti ◽

M. Catto ◽

S. Cellamare ◽

...

Keyword(s):

Free Energy ◽

Interaction Energy ◽

Binding Free Energy ◽

Linear Interaction ◽

Linear Interaction Energy ◽

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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 ◽

Author(s):

A. Bortolato ◽

S. Moro

Keyword(s):

Free Energy ◽

Interaction Energy ◽

In Silico ◽

Binding Free Energy ◽

Linear Interaction ◽

Linear Interaction Energy ◽

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Application of the linear interaction energy method (LIE) to estimate the binding free energy values of Escherichia coli wild-type and mutant arginine repressor C-terminal domain (ArgRc)–l-arginine and ArgRc–l-citrulline protein–ligand complexes

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2003.09.003 ◽

2004 ◽

Vol 22 (4) ◽

pp. 249-262 ◽

Author(s):

A.M. Asi ◽

N.A. Rahman ◽

A.F. Merican

Keyword(s):

Escherichia Coli ◽

Free Energy ◽

Interaction Energy ◽

Energy Method ◽

Binding Free Energy ◽

Wild Type ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Terminal Domain ◽

Arginine Repressor

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Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-017-0055-0 ◽

2017 ◽

Vol 32 (1) ◽

pp. 239-249 ◽

Author(s):

Eko Aditya Rifai ◽

Marc van Dijk ◽

Nico P. E. Vermeulen ◽

Daan P. Geerke

Keyword(s):

Free Energy ◽

Interaction Energy ◽

Binding Free Energy ◽

Reliability Estimation ◽

Farnesoid X Receptor ◽

Grand Challenge ◽

Linear Interaction ◽

Linear Interaction Energy

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Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2020.00114 ◽

2020 ◽

Vol 7 ◽

Author(s):

Eko Aditya Rifai ◽

Marc van Dijk ◽

Daan P. Geerke

Keyword(s):

Free Energy ◽

Interaction Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Energy Calculations ◽

Recent Developments ◽

Binding Free Energy Calculations

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Binding free energy calculation of peptides to carbon nanotubes using molecular dynamics with a linear interaction energy approach

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2009.07.018 ◽

2009 ◽

Vol 913 (1-3) ◽

pp. 63-69 ◽

Author(s):

Anahita Kyani ◽

Bahram Goliaei

Keyword(s):

Carbon Nanotubes ◽

Molecular Dynamics ◽

Free Energy ◽

Interaction Energy ◽

Binding Free Energy ◽

Energy Approach ◽

Free Energy Calculation ◽

Energy Calculation ◽

Linear Interaction ◽

Linear Interaction Energy

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Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method

Journal of Chemical Theory and Computation ◽

10.1021/ct800404f ◽

2009 ◽

Vol 5 (2) ◽

pp. 380-395 ◽

Author(s):

Göran Wallin ◽

Martin Nervall ◽

Jens Carlsson ◽

Johan Åqvist

Keyword(s):

Free Energy ◽

Interaction Energy ◽

Energy Method ◽

Large Scale ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Energy Calculations ◽

Binding Free Energy Calculations

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How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.0c00934 ◽

2020 ◽

Vol 60 (12) ◽

pp. 6624-6633

Author(s):

Dongxiao Hao ◽

Xibing He ◽

Beihong Ji ◽

Shengli Zhang ◽

Junmei Wang

Keyword(s):

Free Energy ◽

Interaction Energy ◽

Energy Method ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Energy Calculations ◽

Binding Free Energy Calculations

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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 ◽

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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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 ◽

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 ◽

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Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models

Journal of Computational Chemistry ◽

10.1002/jcc.23081 ◽

2012 ◽

Vol 33 (29) ◽

pp. 2340-2350 ◽

Author(s):

Sushil Kumar Mishra ◽

Johan Sund ◽

Johan Åqvist ◽

Jaroslav Koča

Keyword(s):

Interaction Energy ◽

Computational Prediction ◽

Free Energies ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Energy Models ◽

Binding Free Energies

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