Visualize sequence conservation on predicted structures.
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- Dominant language
- HTML
- Stars
- 115
- Forks
- 75
- PR merge metrics
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Description
Description of feature
It can be useful to visualize sequence conservation projected on to 3D structures. Geometric clusters of conserved surface residues often correspond with functional sites so this visualization can be informative.
Within proteinfold, we already generate MSAs which can be used for sequence conservation and we already have output structures. It seems natural to project conservation values on to the output structures to support this analysis.
One existing tool that is used for this purpose is consurf. There is a standalone implementation but I did not see a license file.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the existing multiple-sequence-alignment generation and predicted-structure output stages in the proteinfold workflow. Review how both outputs are represented and determine the requirements for projecting conservation onto the structures; done should produce an integrated visualization of conservation on the predicted 3D structures.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100