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

Anahita Kyani; Bahram Goliaei

doi:10.1016/j.theochem.2009.07.018

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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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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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 ◽

Linear Interaction Energy

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Insights into the mechanism of inhibition of phospholipase A2 by resveratrol: An extensive molecular dynamics simulation and binding free energy calculation

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2020.107649 ◽

2020 ◽

Vol 100 ◽

pp. 107649

Author(s):

Sajedeh Sharifpour ◽

Sara Fakhraee ◽

Reza Behjatmanesh-Ardakani

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Phospholipase A2 ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Mechanism Of Inhibition

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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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Molecular dynamics and high throughput binding free energy calculation of anti-actin anticancer drugs—New insights for better design

Computational Biology and Chemistry ◽

10.1016/j.compbiolchem.2016.05.008 ◽

2016 ◽

Vol 64 ◽

pp. 47-55 ◽

Cited By ~ 3

Author(s):

Roopa. L ◽

Pravin Kumar. R ◽

Sudheer Mohammed M.M.

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Anticancer Drugs ◽

High Throughput ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation

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Understanding the structural and energetic basis of inhibitor and substrate bound to the full-length NS3/4A: insights from molecular dynamics simulation, binding free energy calculation and network analysis

Molecular BioSystems ◽

10.1039/c2mb25157d ◽

2012 ◽

Vol 8 (10) ◽

pp. 2753 ◽

Cited By ~ 22

Author(s):

Weiwei Xue ◽

Meixia Wang ◽

Xiaojie Jin ◽

Huanxiang Liu ◽

Xiaojun Yao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Network Analysis ◽

Binding Free Energy ◽

Full Length ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation

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3D-QSAR-aided design of potent c-Met inhibitors using molecular dynamics simulation and binding free energy calculation

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1479309 ◽

2018 ◽

Vol 37 (8) ◽

pp. 2165-2178 ◽

Cited By ~ 4

Author(s):

Pavithra K. Balasubramanian ◽

Anand Balupuri ◽

Swapnil P. Bhujbal ◽

Seung Joo Cho

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

3D Qsar ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Aided Design

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