ColabFold

1.5.5

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• Terminal:

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• Editor:

• Package Manager:

• Programming Language:

• NVIDIA Libraries:

• Extension:

1.4.0

• Operating System:

• Terminal:

• Shell:

• Editor:

• Package Manager:

• Programming Language:

• NVIDIA Libraries:

• Extension:

ColabFold is an emerging protein folding prediction tool based on Google DeepMind’s AlphaFold2.

ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold.

For more information check here.

Note

AlphaFold2 and ColabFold do not support multiple GPUs: Only one GPU can model a protein.

Runtime

The app is deployed into four different modes:

1. Lab:

   • Runs AlphaFold2 using MMseqs2 within a JupyerLab interactive session.

   • AlphaFold2 weights stored in /colabfold/params.

   • Tutorial notebooks available in /colabfold/notebooks.

2. Prediction:

   • Generates MSAs for small scale local structure/complex predictions using the MSA server database.

   • Runs AlphaFold2 prediction using MSAs generated through MMseqs2.

   • Local PDB database stored in /colabfold/databases/pbd/divided.

   • AlphaFold2 weights stored in /colabfold/params.

   Hint

   GPU intensive process.

3. Search:

   • Generates MSAs for large scale structure/complex predictions.

   • Runs MMseqs2 locally: takes input .fasta file, outputs .a3m file.

   • Databases for MMseq2 search available in /colabfold/databases.

   Hint

   CPU intensive process.

4. Split MSAs: Splits a single search into one .a3m file per MSA.