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I'm trying to calculate ligand-aminoacid interaction from OpenMM simulation from pdb topology and xtc trajectory. Ligand structure is show below
![image](https://github.com/chemosim-lab/ProLIF/assets…
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e.g., maybe in context of the refactoring or the ID datastructure visualization
Ask me if you need the code to produce something like this (here some protein/peptide visualization from mzTab):
![ima…
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To replicate, create .txt
```
p65 and p50 form NF-kappaB.
```
.ann
```
T2 Protein 8 11 p50
T4 Heterodimer_association 12 16 form
E1 Heterodimer_association:T4 Reactant:T2
```
the resulting…
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Hello Mol* Team,
I am using Mol*(viewer) to display a protein-ligand complex. Upon mouse-clicking the ligand, could you guide me on how to exclusively reveal the amino acid residues surrounding the…
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- For some reason, the text in some domains is unnecessarily squeezed.
- Since the lengths of proteins are equalized, it is not possible to infer relative lengths in a list of proteins. I sug…
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What a great job! Only the SDF files of small molecules are output in the "results/user_predictions_small" folder when I infer with the example code:
`python -m inference --protein_ligand_csv data/…
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Hello!
I'm using react-vega to render visualizations from a JSON schema. It works well, except when I want to display a vertically concatenated view (using vconcat) that fits the container size and…
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# ePlant3 Interactions View Blueprint and Requirements
by V. Lau (reviewed by N. Provart)
## Introduction
Genes and their gene products (proteins) can interact with other genes and gene produ…
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In essence, this will provide an index of tools useful for making potential manuscript figures, with image examples. It could be divided like this:
**- Genome visualization**
- includes tools u…
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- Integrating MSAView and Protein viewer with genome browsing experience
- Mapping genome coordinates to protein coordinates to visualize impacts, if anyone in the user community has experience wi…