colabfold_af2

Colabfold scripts

Basic scripts to run AF2 with ColabFold.

Predict single fasta/a3m file

Usage

SBATCH predict_single_AF2.sh <input_file (fasta,a3m)> <additional_args (--msa-mode single sequence --num-recycle 16)>

Example

SBATCH predict_single_AF2.sh examples/3HB.fasta --num-recycle 16

Predict pdb files and compare

Adjust the array range accordingly

Usage

Note: ignore binder args if interaction analysis is not required

sbatch predict_pdbs_AF2.sh <input_file (pdb,folder with pdbs)> <binder args (binder,binder-second)> <additional_args (--msa-mode single sequence --num-recycle 16)>

Example

sbatch predict_pdbs_AF2.sh examples/3HB_folder/ binder-second --num-recycle 16