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**Title: End-to-end differentiable learning of protein structure**
Link: https://www.biorxiv.org/content/biorxiv/early/2018/08/29/265231.full.pdf
Code: https://github.com/aqlaboratory/proteinnet
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It looks like this one is missing some assertions that should have passed through the rule:
If R1 has output E1
and E1 regulates R2
then R1 directly provides input for Binding reaction 3
Bindi…
goodb updated
4 years ago
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I am working with a self assebmled system that consists of four ligands bridged together with two Pd(II) ions to form a nano-capsule. Both the ligands and the metals are parameterised with the ffld se…
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Rebecca Foulger created issue - 09-Dec-13 08:23
Rebecca Foulger added a comment - 09-Dec-13 08:27
Most XPs are in gene_ontology_write.obo (for ChEBI ligands) or in x-mf-protein.obo for protein ligand…
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Hello
I have a molecule that I load from a PDB file and I would like to set the color of atoms from their index.
Thank you for your help
```bash
python -c 'import nglview; print(nglview.__ve…
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I analyzed 23 pathways, including 156 reaction to reaction 'nextStep' links. The conversion process captures 120 (77%) of these links as causal relations, losing 36 that cross pathway boundaries.
…
goodb updated
4 years ago
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```cm.fit_transform([[['Br'], [[0, 0, 0]]]])```
=>
```KeyError: 'Br'```
I guess there's a lookup table for charges somewhere, and Br and potentially other atoms are missing from it?
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https://mp.weixin.qq.com/s/x7oYnMgOKUp7OefFbuKcJw
ixxmu updated
3 years ago
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## Idea
I want to formalize the format for storing HDF5 Trajectories on disk, and provide some kind of a "contract" that our code can say that it implements. It makes sense for the writers of traject…
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As part of the GO-CAM specs, binding reactions will not be enabled-by either of the participants, instead all of the 'things' that bind will get has_input relationships to the binding term. We need to…
ukemi updated
4 years ago