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Hello.
I installed g-clip and downloaded all the necessary data and .pt files.
Now how do I proceed further to calculate a binding affinity for arbitrary protein and ligand?
Could you provide some …
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Hi
I was wondering if one can use groamcs-ramd to get binding events instead of unbinding. Is it possible to change the parameters in which the ligand approaches the binding site instead of getti…
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Thanks for the wonderful tool!
This issue might only be about biology, not technology.
In the file new_ligand_receptor_TFs.txt, there are 3 columns: Ligand_Symbol, Receptor_Symbol and TF_Symbol.
In…
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Thank you guys so much for conducting this novel study. I had a few questions about the data. I was able to get the warhead, linker, and E3 ligand data by downloading from PROTAC DB. However, they don…
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Host-guest/protein ligand binding data: Do we use host-guest/protein-ligand data in our fitting? Or just for benchmarking? If so, which systems should we look at?
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In this project, the main key is to find the binding site of the WDR 91 protein. In order to do this, I have decided to delete the ligand from the [8SHJ](https://www.rcsb.org/structure/8SHJ) and decid…
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In the Uni-Mol paper, the average number of seconds per ligand is 0.2.
> Efficiency benchmark We compare Uni-Mol binding pose prediction with popular docking tools in efficiency. The baseline result…
tsa87 updated
12 months ago
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From Wnt pathway discussion (Signaling WS 10/2017)
https://docs.google.com/document/d/1wCzCkPL9ft20ZP5XnTn8IQAcxoFEduaBmzVWKN0hbU0/edit#
Create 2 new terms: “receptor ligand agonist activity” and “…
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I'm concerned that timescales for adequate sampling of ligand motions in the non-interacting state may be sufficiently slow to cause unanticipated problems, and would like to discuss and find out how …
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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…