Merge pull request #270 from KosinskiLab/fix-mmseqs-issue60-issue176-…

…issue177 Fix mmseqs ifixed #60 #176 #177
KosinskiLab · Mar 1, 2024 · 7cf4efb · 7cf4efb
2 parents 9147a2f + 47396b9
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diff --git a/alphapulldown/ColabFold b/alphapulldown/ColabFold
diff --git a/manuals/mmseqs2_manual.md b/manuals/mmseqs2_manual.md
@@ -2,6 +2,7 @@
 
 # option 1: run mmseqs2 remotely 
 
+**Caution**:To avoid overloading the remote server, do not submit a large number of jobs at the same time. If you want to calculate MSAs for many sequences, plese use Option 2 below
 For the purpose of this manual, the expected file is already provided here: [`example_1_sequences.fasta`](../example_data/example_1_sequences.fasta). If you want to run a smaller test, you can use [`example_1_sequences_shorter.fasta`](../example_data/example_1_sequences_shorter.fasta) instead.
 
 :memo: *The example file was generated by downloading all 294 proteins that belong to human translation pathway from: [Reactome](https://reactome.org/PathwayBrowser/#/R-HSA-72766&DTAB=MT). eIF4G2 sequence was downloaded from (Uniprot:[P78344](https://www.uniprot.org/uniprot/P78344)).*
@@ -94,3 +95,6 @@ output_dir
     |-protein_C.pkl
     ...
 ```
+**NOTE** If you used mmseqs2 in either of these 2 options, please remember to cite: 
+Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M. ColabFold: Making protein folding accessible to all.
+Nature Methods (2022) doi: 10.1038/s41592-022-01488-1
+1 −1		.github/workflows/docker.yml
+2 −5		.github/workflows/test.yml
+12 −19		AlphaFold2.ipynb
+1 −1		Dockerfile
+6 −5		ESMFold.ipynb
+1 −1		README.md
+7 −7		RoseTTAFold2.ipynb
+9 −9		batch/AlphaFold2_batch.ipynb
+15 −14		beta/ESMFold_advanced.ipynb
+52 −15		beta/ESMFold_api.ipynb
+71 −14		colabfold/alphafold/models.py
+44 −30		colabfold/batch.py
+18 −3		colabfold/citations.py
+101 −20		colabfold/download.py
+94 −34		colabfold/mmseqs/search.py
+3 −2		colabfold/utils.py
+2,199 −1,771		poetry.lock
+12 −9		pyproject.toml
+15 −1		setup_databases.sh
+2 −0		tests/mock.py
+6 −6		tests/test_colabfold.py
+9 −0		utils/convert_deepfold_weights.py