Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation

Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

International Journal of Molecular Sciences ◽

10.3390/ijms15010798 ◽

2014 ◽

Vol 15 (1) ◽

pp. 798-816 ◽

Cited By ~ 17

Author(s):

C. Ruben Vosmeer ◽

René Pool ◽

Mariël van Stee ◽

Lovorka Perić-Hassler ◽

Nico Vermeulen ◽

...

Keyword(s):

Interaction Energy ◽

Binding Affinity ◽

Energy Approach ◽

Linear Interaction ◽

Binding Affinity Prediction ◽

Affinity Prediction

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 ◽

Cited By ~ 7

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 ◽

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

Journal of Chemical Theory and Computation ◽

10.1021/ct9006025 ◽

2010 ◽

Vol 6 (5) ◽

pp. 1608-1621 ◽

Cited By ~ 12

Author(s):

Traian Sulea ◽

Christopher R. Corbeil ◽

Enrico O. Purisima

Keyword(s):

Free Energy ◽

Interaction Energy ◽

Solvation Free Energy ◽

Linear Interaction ◽

Rapid Prediction ◽

Extensive Test

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 ◽

Ck2 Inhibitors

Binding Affinities for a Series of Selective Inhibitors of Gelatinase-A Using Molecular Dynamics with a Linear Interaction Energy Approach

The Journal of Physical Chemistry B ◽

10.1021/jp0044476 ◽

2001 ◽

Vol 105 (22) ◽

pp. 5304-5315 ◽

Cited By ~ 22

Author(s):

T. J. Hou ◽

W. Zhang ◽

X. J. Xu

Keyword(s):

Molecular Dynamics ◽

Interaction Energy ◽

Energy Approach ◽

Gelatinase A ◽

Binding Affinities ◽

Selective Inhibitors ◽

Linear Interaction ◽

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 ◽

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.7b00222 ◽

2017 ◽

Vol 57 (9) ◽

pp. 2294-2308 ◽

Cited By ~ 8

Author(s):

Marc van Dijk ◽

Antonius M. ter Laak ◽

Jörg D. Wichard ◽

Luigi Capoferri ◽

Nico P. E. Vermeulen ◽

...

Keyword(s):

Cytochrome P450 ◽

Interaction Energy ◽

Binding Affinity ◽

Aromatase Inhibitors ◽

Linear Interaction ◽

Binding Affinity Prediction ◽

Affinity Prediction ◽

P450 Aromatase ◽

Cytochrome P450 Aromatase

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 ◽

Cited By ~ 7

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 ◽

Terminal Domain ◽

Arginine Repressor

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 ◽

Cited By ~ 9

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 ◽

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 ◽

Energy Calculations ◽

Recent Developments ◽

Binding Free Energy Calculations