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From the discussion in #datamodeling:
Eugene: Beyond the obvious PubMed IDs, what kinds of attributes would be considered core standards for provenance? I brought up ECO codes, which a few others a…
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When calculating the binding free energy change caused by mutation of protein amino acids using AMBER's TI for FEP, when calculating the complex, the energy calculated in a certain window is negative …
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Hi everyone,
The repo looks very interesting. I was wondering if you had the pdb structure you started out with and put through tleap that matches the coordinates of the mol2 files.
I think in t…
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**In broad terms, what are you trying to do?**
[BindingDB](http://bindingdb.org) has a very large number (>1M) of binding free affinity measurements that we can use as a source of automating the cura…
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Hi,
I started a job on a small druggable protein using the -n 50 option. How many batches will be generated? The job has been running for 4 h and reached almost 500 batches.
BW/Evert
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Yo Tomas,
I need your library to write out the cif file ([PR](https://github.com/krab1k/ChargeFW2/pull/7) I am submitting).
I am creating a branch to do this, however, I think it would be good …
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Last year at BioITWorld I chatted to sofware vendors who had various snazzy 3D features with a view to them searching some OSM frontrunners. I have to say, beyond polite interest, traction was mor…
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We need to come up with appropriate test systems to evaluate the different methods.
The dataset should contain examples of:
- [ ] Identical sequences, different conformations
- [ ] Homologous s…
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We need a new CLI analysis tool (which can also be run via the Python API) to analyze simulations set up via the perses CLI.
It should provide three major outputs:
1. **Optimal predictions:** The …
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hi Chao Shen,
i am creating another issue as this is different from the other one.
in your paper you mentioned that the performance varies depending on the protein. in real-world use-cases, we …