Skip to content

Latest commit

 

History

History
79 lines (51 loc) · 2.43 KB

README.md

File metadata and controls

79 lines (51 loc) · 2.43 KB

NanoGEN

This project utilizes the Hugging Face Transformers library to design antibody sequences using the PROTGPT2 model. The primary objective is to generate antibody sequences with specific Complementarity-Determining Regions (CDRs) and framework modifications.

Installation

To run this project, you must install Hugging Face:
https://huggingface.co/docs/transformers/en/installation

After install hugging face and it dependencies, install the pre-trained model from ProtGPT2:
https://huggingface.co/nferruz/ProtGPT2/tree/main?library=transformers

Download the repository in your directory

cd your_directory
git clone https://github.com/jsartori12/NanoGEN.git

Running the code

Loading pre-trained model

First go to the "functions_protgpt2.py" and paste the path of the directory containing the pre-trained model in the variable "path_model" 

#### Load directory containing binaries for the pre-trained model

path_model = ""

#### Load pre-trained model and tokenizer
tokenizer = GPT2Tokenizer.from_pretrained(path_model)
model = GPT2LMHeadModel.from_pretrained(path_model)

Designing CDRs or frameworks

generate_new_protgpt2.py is used to design CDRs for a given antibody or design frameworks residues flanking the CDRs.
Follow below a usage example of the function: 

####### Loading libraries
from transformers import pipeline
from transformers import GPT2LMHeadModel, GPT2Tokenizer
from typing import List
from tqdm import tqdm
import functions_protgpt2


#### Input antibody sequence
input_text = "MADVQLQASGGGLVQAGGSLRLSCAASGNINTIDVMGWYRQAPGKQRELVADITRLASANYADSVKGRFTISRDNAKNTVYLQMNNLEPKDTAVYYCAQWILSTDHSYMHYWGQGTQVTVTVSS"


#### List of CDRs indexs
cdrs = [25,26,27,28,29,30,31,51,52,53,54,55,94,95,96,97,98,99,100,101,102,103,104,105]

#### Designing CDRs residues for a given antibody sequence
design_cdrs = functions_protgpt2.Create_sequences(input_text = input_text, 
                                                cdrs_list = cdrs,
                                                design_type = "cdr")

#### Designing 3 framework residues flanking the CDRs for a given antibody sequence
design_framework = functions_protgpt2.Create_sequences(input_text = input_text, 
                                                cdrs_list = cdrs,
                                                design_type = "fm",
                                                flank_size = 3)