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[Ruiter, Anita de, and Chris Oostenbrink. “Advances in the Calculation of Binding Free Energies.” *Current Opinion in Structural Biology* 61 (2020): 207–12.](https://doi.org/10.1016/j.sbi.2020.01.016)
cramg updated
3 years ago
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Dear OpenMM team,
I am looking for a package/tutorial to do protein-protein binding free energies. I have found plenty of alchemical methods for protein-ligand but none for protein-protein. Any poi…
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Hello,
When calculating the free energy change for a perturbation involving only dummy atoms to dummy atoms, MBAR gives exactly zero kcal/ mol, as expected, whereas TI gives positive free energies …
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[Hayes, Joseph M., and Georgios Archontis. "MM-GB (PB) SA calculations of protein-ligand binding free energies." Molecular Dynamics-Studies of Synthetic and Biological Macromolecules (2012): 171-190](…
cramg updated
3 years ago
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@jchodera will draft a proposal on this issue for representing free energies and uncertainties (of various flavors) that generalize well across different alchemical protocols. We'll use that proposal …
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We should check the error induced in computed binding free energies by using `CutoffNonPeriodic` with various cutoff radii.
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You should take the fraction_contacts_expectation function in secondary_structure.py as the example. Instead of passing in a native contact list and a distance cutoff, you pass in a general function …
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**Gammapy version**
1.0.1
**Bug description**
Probably not a bug per-se, but somewhat unexpected to see
energy_edges in Light curve estimator seem to be force using energy edges aligned to I…
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"Bootstrap (formerly Twitter Bootstrap) is a [free and open-source](https://en.wikipedia.org/wiki/Free_and_open-source) [CSS framework](https://en.wikipedia.org/wiki/CSS_framework) directed at respons…
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Currently, free energy is computed by the edges who query the connected nodes. However, deterministic nodes have no free energy.
This becomes a problem in equality nodes. Suppose we have 3 edges x…