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

Perturbation Approach ◽

Linear Interaction ◽

Energy Calculations ◽

One Step

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 ◽

Linear Interaction ◽

Energy Calculations ◽

Recent Developments ◽

Binding Free Energy Calculations

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 ◽

Linear Interaction ◽

Energy Calculations ◽

Binding Free Energy Calculations

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 ◽

Linear Interaction ◽

Energy Calculations ◽

Binding Free Energy Calculations

Analysis of α4 β1integrin specific antagonists binding modes: structural insights by molecular docking, molecular dynamics and linear interaction energy method for free energy calculations

Journal of the Brazilian Chemical Society ◽

10.1590/s0103-50532010000300022 ◽

2010 ◽

Vol 21 (3) ◽

pp. 546-555 ◽

Cited By ~ 5

Author(s):

João Hermínio Martins da Silva ◽

Laurent Emmanuel Dardenne ◽

Wilson Savino ◽

Ernesto Raul Caffarena

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Docking ◽

Interaction Energy ◽

Energy Method ◽

Binding Modes ◽

Linear Interaction ◽

Energy Calculations ◽

Structural Insights

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 ◽

Linear Interaction ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations

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

QligFEP: an automated workflow for small molecule free energy calculations in Q

Journal of Cheminformatics ◽

10.1186/s13321-019-0348-5 ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 13

Author(s):

Willem Jespers ◽

Mauricio Esguerra ◽

Johan Åqvist ◽

Hugo Gutiérrez-de-Terán

Keyword(s):

Free Energy ◽

Small Molecule ◽

Energy Calculations

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 ◽

Linear Interaction Energy

Probing the interaction mechanism of small molecule inhibitors with matriptase based on molecular dynamics simulation and free energy calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2016.1160259 ◽

2016 ◽

Vol 35 (4) ◽

pp. 755-764 ◽

Cited By ~ 4

Author(s):

Dong-Ru Sun ◽

Qing-Chuan Zheng ◽

Hong-Xing Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Small Molecule ◽

Small Molecule Inhibitors ◽

Interaction Mechanism ◽

Dynamics Simulation ◽

Energy Calculations