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See https://github.com/cmungall/capital-offence/issues/1
We should always use "type" not "Type"
- [GO:0004909](http://purl.obolibrary.org/obo/GO_0004909) ! interleukin-1, **Type** I, activating rec…
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I am trying to install Autdock Vina 1.2.3. I have used `chmod` to solve the `Permission denied` error. However I was faced with an additional issue as shown below:
I have tried 1.2.2 and 1.2.0 and …
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Hi,
I am new to mdtraj. I performed MD with desmond. But, when I try to use mdtraj to analyze it.
The out.cms file (topology from desmond) cannot be recognized by the mdtraj...
I tried to convert …
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The best-binding algorithm always gives C5 - PHE206 as the best binding pair, but that part of the binding pocket doesn't have enough space for the ligand, causing it to clash with various residues an…
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Hello,
I have been looking into the CDK2 test set and I ended up having some numerical issues related to high clashes between some of the ligands (`1h1s`, `28` and `29`). I have attached an example…
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### Model Name
ImageMol
### Model Description
Representation Learning Framework that utilizes molecule images for encoding molecular inputs as machine readable vectors for downstream tasks su…
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Currently, when putrescine or cadaverine are docked inside TAAR6 or TAAR8, only one of the receptor's two amino-binding ASP residues is coordinated to the ligand's amino groups. One of the ASPs is loc…
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Hi,
Thank you for the amazing work!
I am curious about how to segment the protein and how to choose the native block for a protein-ligand pair.
1. As mentioned in Sec 3.4, "We, therefore, take f…
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I think I am running out of memory even with 392GB for running standard pipeline for molecules size of ribociclib (62 atoms). The input for python poltype.py is:
```
structure=ribociclib.sdf
scrat…
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Hi，
I'm still a newbie in ligand-receptor binding. I did an experiment on translation equivariance in the 5ol3 complex in PDBBind dataset. I experimented with a translation of both ligand and recep…