SPEACH_AF

Sampling Protein Ensembles and Conformational Heterogeneity with Alphafold2

Files

SPEACH_AF_scan (jupyter notebook): will generate modified MSA files (alanine mutagenesis) based on an initial MSA and PDB requires: Bio, numpy, copy

To run multiple copies use the following command (this replaces the modified batch.py file):
Colabfold_batch input output --num-seeds X

Data Directory

Data files associated with SPEACH_AF paper

References

Paper

• Stein, SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2.
  PLoS Comput Biol (2022) 18(8), e1010483 doi: 10.1371/journal.pcbi.1010483

If using ColabFold and Alphafold do not forget to cite these references and any associated references from using ColabFold

• Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M. ColabFold - Making protein folding accessible to all.
  Nat Methods (2022) 19(6), 679-682. doi: 10.1038/s41592-022-01488-1
• Jumper et al. "Highly accurate protein structure prediction with AlphaFold."
  Nature (2021) 596, 583–589. doi: 10.1038/s41586-021-03819-2