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Currently, the input argument logic for `energy_func` is not clean.
In `RotamerEnsemble.py`, it is called as `self.energy_func(self.protein, self)` and `self.energy_func(temp_ensemble.protein, temp…
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Hello everyone,
I am creating Molecule object from a rdkit mol,with a conformer file,ligand.mol2 and a protein file 5x1a.pdb, after merging it to a complex file 5x1a_complex.pdb, it is impossible t…
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(Follow-up from #51)
The PHI-base team has recently reviewed the Pathogen and Host sections of the gene page and identified a number of problems. We've decided to clarify the requirements for these…
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**_Integral Retrospective Correction (IRC) (updated July 16, 2023)_**:
- Integral-retrospective-correction (IRC) is an experimental modification of the Loop's [Retrospective Correction](https://lo…
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*************edited November 20***************
**TRACKER**
BA.2.86: -C6541T,A7842, C8293T, G8393A (new query thx to @aviczhl2 )
JN.1 QUERY: C18894T, T15756A, A7842, -C6541T
XDD Query : C6541T…
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## Describe the issue
Hi,
using VEP web api, i'm about to find some specific genomic coordinate from HGVS.
but some of them, vep could not find these.
for example, Gen1:p.K707N was not found on B…
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Hi
I am trying to run your example (i.e. Spike) in order to get heatmap/distribution:
`ddg2heatmap -p ../../wt/saturation_scan/6LZGab_noHOH.pdb -d ../../wt/saturation_scan/results/interface_ddgs/…
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I am getting very inconsistent results when I vary the `points` (or `times`) parameter in `Roadrunner.simulate`. Solutions diverge significantly after a certain time frame.
I have a custom SBML fil…
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Hello, I have been using AlphaFold from container on HPC system for a couple of months and it has really shown to be useful. Just recently started doing predictions on multimers (in my case mAb drugs)…
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Hi,
Thanks for your paper and the code. Could you provide an example showing how to dock two proteins where both are pdb files?
Thanks!