sokrypton / sokrypton/ColabFold
How to get the PDB or template released data information?
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Description
Expected Behavior
When I using ColabFold: AlphaFold2 using MMseqs2 (ColabFold v1.2 , model_type: AF2-multimer) with "use_templates" option, I found my predicted structure is much better than without "use_templates" .
So, I worried about weather this PDB quries's tempalte was included in current ColabFold databse. But I can't figiure out how to check the PDB tempalte released data in ColabFold.
Is ColabFold using the newest PDB70 databse like 2021-08~ or in line with the AF2-multimer preprint's trainning data 2018-04-30?https://deepmind.com/research/publications/2021/protein-complex-prediction-with-alphafold-multimer
Many thanks!
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
No file, test, or entry point is identified in the issue. Review the ColabFold template and database documentation, then verify how the PDB70 release date is exposed and whether the documented information answers the question about AF2-multimer training data.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100