CBTOPE2: Prediction of interactivity of antigens in protein sequence

This repository contains the standalone code for CBTOPE2 prediction tool. CBTOPE2 is an antibody interacting residues predictor. To support the scientific community, we have developed a standalone software and web server for the tool. For a user-friendly access to CBTOPE2, please use https://webs.iiitd.edu.in/raghava/cbtope2/.

Installation (dependencies)

1. Standalone

Download standalone zip file from https://webs.iiitd.edu.in/raghava/cbtope2/standalone.html

1. Unzip the zip file you just downloaded

2. pip install Bio joblib sklearn openpyxl
   

3. Execute:

   python standalone.py [-i INPUT] [filename.fasta] [-t probability threshold = 0.5] [-m {1,2}]
   

   Optional arguments:

• -i INPUT, --input INPUT
  Input: Protein or peptide sequence(s) in FASTA format or a single sequence per line in single-letter code.
  Input File: Allows users to provide input in FASTA format.

• -t THRESHOLD, --threshold THRESHOLD
  Threshold: Value between 0 to 1 (default is 0.5).
  Threshold: User should provide a threshold between 0 and 1; by default, it is 0.5.

• -m {1,2}, --model {1,2}
  Model Type:
  1: PSSM-based model
  2: RSA + PSSM ensemble model (Best Model).
  Model: User can choose between two models: 1 for PSSM-based, and 2 for RSA + PSSM ensemble.

OR

2. PIP package

To install the dependency - SPOT-1D-Single, use the following commands in the same order:

1. Clone the repository:

   git clone https://github.com/jas-preet/SPOT-1D-Single.git
   

2. Move into the directory:

   cd SPOT-1D-Single
   

3. Download the model checkpoints:

   wget https://apisz.sparks-lab.org:8443/downloads/Resource/Protein/2_Protein_local_structure_prediction/jits.tar.xz
   

4. Extract the files:

   tar -xvf jits.tar.xz
   

5. Create a conda environment:

   conda create -n cbtope2_env python=3.7
   

6. Activate the environment:

   conda activate cbtope2_env
   

7. Install PyTorch:

   • If using GPU:

     conda install pytorch==1.6.0 torchvision==0.7.0 cudatoolkit=10.1 -c pytorch
     

   • For CPU only:

     conda install pytorch==1.6.0 torchvision==0.7.0 cpuonly -c pytorch
     

8. Install pandas:

   conda install pandas=1.1.1
   

(Refer to https://github.com/jas-preet/SPOT-1D-Single/tree/master for details.)

9. Install PSSM dependency: You can install system-specific ncbi psi-blast files from https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

10. Install CBTOPE2 package:

    pip install cbtope-2