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

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

Atomistic Prediction of Sorption Free Energies of Cationic Aromatic Amines on Montmorillonite: A Linear Interaction Energy Method

2014 ◽  
Vol 1 (6) ◽  
pp. 284-289 ◽  
Author(s):  
Milinda Samaraweera ◽  
William Jolin ◽  
Dharni Vasudevan ◽  
Allison A. MacKay ◽  
José A. Gascón
Keyword(s):  
Interaction Energy ◽  
Energy Method ◽  
Aromatic Amines ◽  
Free Energies ◽  
Linear Interaction ◽  
Linear Interaction Energy

Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson–Boltzmann and linear interaction energy approximations

2005 ◽  
Vol 363 (1833) ◽  
pp. 2037-2053 ◽  
Author(s):  
Shunzhou Wan ◽  
Peter V Coveney ◽  
Darren R Flower
Keyword(s):  
Free Energy ◽  
T Cell ◽  
Interaction Energy ◽  
T Cell Receptor ◽  
Cell Receptor ◽  
Thermodynamic Integration ◽  
Free Energies ◽  
Linear Interaction ◽  
Poisson Boltzmann ◽  
Binding Free Energies

The binding to the T cell receptor of wild-type and variant HTLV-1 Tax peptide complexed to the major histocompatibility complex has been investigated by means of molecular dynamics simulations. The binding free energy difference is calculated using the molecular mechanics Poisson–Boltzmann surface area and linear interaction energy methods. These methods extract useful information on the binding energetics from simulations of the physical states of the ligands, which are more computationally expedient than the commonly used thermodynamic integration method. The successful reproduction of the relative binding free energies shows that these methods can be useful for free energy calculations and the rational design of drugs and vaccines.

Estimation of the Binding Free Energy by Linear Interaction Energy Models

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 ◽  
Energy Models
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