scholarly journals Equilibrium and Nonequilibrium Foundations of Free Energy Computational Methods

2002 ◽  
pp. 287-303 ◽  
Author(s):  
C. Jarzynski
Keyword(s):  
Free Energy ◽  
Computational Methods

Free Energy of Ligand Binding to Protein: Evaluation of the Contribution of Water Molecules by Computational Methods

2004 ◽  
Vol 11 (23) ◽  
pp. 3093-3118 ◽  
Author(s):  
Pietro Cozzini ◽  
Micaela Fornabaio ◽  
Anna Marabotti ◽  
Donald Abraham ◽  
Glen Kellogg ◽  
...  
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Computational Methods ◽  
Water Molecules

scholarly journals Evaluating the use of absolute binding free energy in the fragment optimization process.

2022 ◽  
Author(s):  
Irfan Alibay ◽  
Aniket Mangakar ◽  
Daniel Seeliger ◽  
Philip Biggin
Keyword(s):  
Free Energy ◽  
Computational Methods ◽  
Binding Free Energy ◽  
Optimization Process ◽  
Energy Estimates ◽  
Free Energies ◽  
Chemical Modifications ◽  
The Right ◽  
Absolute Binding Free Energy ◽  
Binding Free Energies

Key to the fragment optimization process is the need to accurately capture the changes in affinity that are associated with a given set of chemical modifications. Due to the weakly binding nature of fragments, this has proven to be a challenging task, despite recent advancements in leveraging experimental and computational methods. In this work, we evaluate the use of Absolute Binding Free Energy (ABFE) calculations in guiding fragment optimization decisions, retrospectively calculating binding free energies for 59 ligands across 4 fragment elaboration campaigns. We first demonstrate that ABFEs can be used to accurately rank fragment-sized binders with an overall Spearman’s r of 0.89 and a Kendall τ of 0.67, although often deviating from experiment in absolute free energy values with an RMSE of 2.75 kcal/mol. We then also show that in several cases, retrospective fragment optimization decisions can be supported by the ABFE calculations. Cases that were not supported were often limited by large uncertainties in the free energy estimates, however generally the right direction in ΔΔG is still observed. Comparing against cheaper endpoint methods, namely Nwat-MM/GBSA, we find that ABFEs offer better outcomes in ranking binders, improving correlation metrics, although a similar confidence in retrospective synthetic decisions is achieved. Our results indicate that ABFE calculations are currently at the level of accuracy that can be usefully employed to gauge which fragment elaborations are likely to offer the best gains in affinity.

Encultured minds, not error reduction minds

2020 ◽  
Vol 43 ◽  
Author(s):  
Robert Mirski ◽  
Mark H. Bickhard ◽  
David Eck ◽  
Arkadiusz Gut
Keyword(s):  
Free Energy ◽  
Error Reduction ◽  
Energy Principle ◽  
Free Energy Principle ◽  
Current Article

Abstract There are serious theoretical problems with the free-energy principle model, which are shown in the current article. We discuss the proposed model's inability to account for culturally emergent normativities, and point out the foundational issues that we claim this inability stems from.

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