scholarly journals Binding Free Energy Landscape of Domain-Peptide Interactions

2011 ◽  
Vol 7 (8) ◽  
pp. e1002131 ◽  
Author(s):  
Iskra Staneva ◽  
Stefan Wallin
Keyword(s):  
Free Energy ◽  
Binding Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Peptide Interactions ◽  
Domain Peptide

scholarly journals Imaging G protein–coupled receptors while quantifying their ligand-binding free-energy landscape

2015 ◽  
Vol 12 (9) ◽  
pp. 845-851 ◽  
Author(s):  
David Alsteens ◽  
Moritz Pfreundschuh ◽  
Cheng Zhang ◽  
Patrizia M Spoerri ◽  
Shaun R Coughlin ◽  
...  
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
G Protein ◽  
Binding Free Energy ◽  
Energy Landscape ◽  
G Protein Coupled Receptors ◽  
Free Energy Landscape ◽  
G Protein Coupled

scholarly journals Simultaneous prediction of binding free energy and specificity for PDZ domain–peptide interactions

2013 ◽  
Vol 27 (12) ◽  
pp. 1051-1065 ◽  
Author(s):  
Joseph J. Crivelli ◽  
Gordon Lemmon ◽  
Kristian W. Kaufmann ◽  
Jens Meiler
Keyword(s):  
Free Energy ◽  
Binding Free Energy ◽  
Pdz Domain ◽  
Peptide Interactions ◽  
Simultaneous Prediction ◽  
Domain Peptide

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

The Perturbed Free Energy Landscape: Linking Ligand Binding to Biomolecular Folding

ChemBioChem ◽  
2020 ◽  
Author(s):  
fareed aboul-ela ◽  
Abdallah S Abdelsatter ◽  
Youssef Mansour
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Energy Landscape ◽  
Free Energy Landscape
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