NABind

Usage

To use NABind, please follow the instructions below:

  1. Prepare your input data in pdb format.
  2. Change the paths of required softwares and related databases at config/config.json
  3. Run the NABind command with the appropriate options and input files: python predict.py --pdb ./demo/6chv_D.pdb --outdir ./demo/ --type DNA --structure native
  4. Inspect the output file (result.txt) for the predicted binding sites.

OR use docker image:

  • docker load -i nabind_image.tar
  • docker run -it -v your/uniref90_for_blast:/app/db/u90 -v your/uniclust30_for_hhblits:/app/db/u30 -v downloaded/templatedb/BioLip:/app/db/template/BioLip -v download/esm/model:/app/db/esm -v downloaded/pre-trained/model:/app/model nabindv1hzau
  • python code/predict.py