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

Obaidur Rahaman; Trilce P. Estrada; Douglas J. Doren; Michela Taufer; Charles L. Brooks; Roger S. Armen

doi:10.1021/ci1003009

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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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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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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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 ◽

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 ◽

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 ◽

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 ◽

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 ◽

Linear Interaction Energy

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Efficient free energy calculations on small molecule host-guest systems-A combined linear interaction energy/one-step perturbation approach

Journal of Computational Chemistry ◽

10.1002/jcc.21116 ◽

2009 ◽

Vol 30 (2) ◽

pp. 212-221 ◽

Cited By ~ 24

Author(s):

Chris Oostenbrink

Keyword(s):

Free Energy ◽

Interaction Energy ◽

Small Molecule ◽

Free Energy Calculations ◽

Perturbation Approach ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Energy Calculations ◽

One Step

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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 ◽

Cited By ~ 10

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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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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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 ◽

Linear Interaction Energy ◽

Rapid Prediction ◽

Extensive Test

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