Faculty Opinions recommendation of Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

2004 ◽  
Author(s):  
Rebecca Wade
Keyword(s):  
Free Energy ◽  
Protein Complex ◽  
Energy Estimates

SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

2020 ◽  
Author(s):  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Computational Modelling ◽  
Free Energy Calculations ◽  
Energy Estimates ◽  
Binding Affinities ◽  
Spherical Coordinates ◽  
Collective Variables ◽  
Guest Binding ◽  
Starting Point ◽  
Sampl Challenge

Host-guest binding remains a major challenge in modern computational modelling. The newest 7<sup>th</sup> statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and predict the binding affinities in all three host-guest binding cases of the 6<sup>th</sup> SAMPL challenge. In this work, we employed the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The predicted binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations.

On the van der Waals–Cahn–Hilliard phase-field model and its equilibria conditions in the sharp interface limit

2010 ◽  
Vol 140 (6) ◽  
pp. 1161-1186 ◽  
Author(s):  
Wolfgang Dreyer ◽  
Christiane Kraus
Keyword(s):  
Free Energy ◽  
Phase Field ◽  
Field Model ◽  
Van Der Waals ◽  
Phase Field Model ◽  
Entropy Inequality ◽  
Sharp Interface ◽  
Energy Estimates ◽  
Sharp Interface Limit ◽  
Entropy Flux

We study the thermodynamic consistency of phase-field models, which include gradient terms of the density ρ in the free-energy functional such as the van der Waals–Cahn–Hilliard model. It is well known that the entropy inequality admits gradient and higher-order gradient terms of ρ in the free energy only if either the energy flux or the entropy flux is represented by a non-classical form. We identify a non-classical entropy flux, which is not restricted to isothermal processes, so that gradient contributions are possible.We then investigate equilibrium conditions for the van der Waals–Cahn–Hilliard phase-field model in the sharp interface limit. For a single substance thermodynamics provides two jump conditions at the sharp interface, namely the continuity of the Gibbs free energies of the adjacent phases and the discontinuity of the corresponding pressures, which is balanced by the mean curvature. We show that these conditions can be also extracted from the van der Waals–Cahn–Hilliard phase-field model in the sharp interface limit. To this end we prove an asymptotic expansion of the density up to the first order. The results are based on local energy estimates and uniform convergence results for the density.

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