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I tried to calculate an edge that does not have a perfect mapping and got two error messages. Can you please explain the meaning behind them? What exactly is the issue here?
- 0_easy_rbfe_A_complex…
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This may be a tricky issue to solve.
When using a path based dock, there is a drift that nudges the ligand towards the current path node. If the ligand has formed a bond with the receptor, that bon…
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Dear Dr Judemir Ribeiro,
I'm pretty interested in your recently published tool dr-sasa, which can be used to calculate solvent-accessible surface area (SASA).
In my study, I want to calculat…
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I want to try to simplify the way standard state corrections are incorporated in Yank, and was hoping to get suggestions from @luirink and @davidlmobley.
For generality, Yank uses the concept of "pha…
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Hi Openforcefield,
No question here, just thought I would share some code I used recently to add a ligand to a GPCR binding site. OFF was useful in a recent med chem paper (online shortly) using MD t…
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How feasible would the following algorithm be?
Suppose the docking space (the box containing the binding pocket) were divided into 0.67Å voxels. Each atom of the ligand can then be given a probabil…
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Hello,
I really enjoyed the paper and am trying to implement this method to score several novel protein-ligand interactions that are not part of the training data. I have trained the model and am n…
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## Is Your Feature Request Related to a Problem? Please Describe.
using the obsidian-citation plugin and Better BibLatex export, I would like the frontmatter under the the {{keywords}} (technically…
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Hi,
I was wondering if I could use AutoDock Vina scoring functions to evaluate protein-peptide complexes.
I used Python-based scripts from the AutoDock Vina website just for scoring the complexes.…
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The best-binding is failing for aldehydes. It should favor pairing them with basic side chains, but it is pairing them to acids instead.
_Originally posted by @ssepeq in https://githu…