ProtGPT3-1.3B is a single-sequence autoregressive protein language model for protein sequence generation. It is part of the ProtGPT3 family, an open-source suite of promptable and aligned protein language models ranging from 112M to 10B parameters. ProtGPT3 models use a causal Mixtral-style Mixture-of-Experts architecture and are trained for causal language modeling on protein sequences.

The single-sequence ProtGPT3 models can generate proteins in either N-to-C or C-to-N direction using special directional tokens. The model is intended for unconditional or prefix-conditioned protein sequence generation and can be used as a base model for downstream protein design workflows.

Also consider using the ProtGPT3-1.3B -dpo version for an equivalent model size, but with improved sequence generation.

Model Modalities

N-to-C vs C-to-N:ProtGPT3-1.3B has been trained to process single protein sequences in both N-to-C and C-to-N directions, via two special "directional" tokens, "1" for N-to-C and "2" for C-to-N which which should be placed at the start of the protein sequence (i.e., after the BOS toke) to select the direction.

We provide some examples below.

Uses

How to Get Started with the Model

Install dependencies:

pip install transformers accelerate torch

Load the model and tokenizer:

python

import torch
from transformers import AutoTokenizer, AutoModelForCausalLM

model_id = "AI4PD/ProtGPT3-1.3B"  # Replace with the final checkpoint name

# Load tokenizer for generation
tokenizer = AutoTokenizer.from_pretrained(model_id, trust_remote_code=True,add_bos_token=True, add_eos_token=False, padding_side="left")

model = AutoModelForCausalLM.from_pretrained(
    model_id,
    torch_dtype=torch.bfloat16,
    device_map="auto",
    trust_remote_code=True,
)

model.eval()

Uncoditional generate of protein sequences

python

import torch

prompt = ""  # Optionally provide an amino-acid prefix or model-specific direction

inputs = tokenizer(prompt, return_tensors="pt").to(model.device)

with torch.no_grad():
    output_ids = model.generate(
        inputs["input_ids"],
        max_new_tokens=512,
        do_sample=True,
        temperature=0.8,
        top_p=0.9,
        eos_token_id=tokenizer.eos_token_id,
        pad_token_id=tokenizer.pad_token_id,
        num_return_sequences=20, # set to desired number of protein sequences to be generated in parallel
    )

sequence = tokenizer.decode(output_ids[0], skip_special_tokens=True)
print(sequence) # output includes directional token "1" or "2" to denote if sequence was generated N-to-C or C-to-N

Generate from an amino-acid prefix

python

import torch

# forward N-to-C generation with special token "1" 
prefix = "1MKT" # use special token "2" instead of "1" for reverse  C-to-N generation

inputs = tokenizer(prefix, return_tensors="pt").to(model.device)

with torch.no_grad():
    output_ids = model.generate(
        inputs["input_ids"],
        max_new_tokens=256,
        do_sample=True,
        temperature=0.8,
        top_p=0.9,
        eos_token_id=tokenizer.eos_token_id,
        pad_token_id=tokenizer.eos_token_id,
        num_return_sequences=20, # set to desired number of protein sequences to be generated in parallel
    )

sequence = tokenizer.decode(output_ids[0], skip_special_tokens=True)
print(sequence)

Batch generation

python

import torch

prompts = [
    "",
    "1MKT", # N-to-C generation
    "2MAV", # C-to-N generation
]

inputs = tokenizer(
    prompts,
    return_tensors="pt",
    padding=True,
).to(model.device)

with torch.no_grad():
    output_ids = model.generate(
        inputs["input_ids"],
        max_new_tokens=256,
        do_sample=True,
        temperature=0.8,
        top_p=0.9,
        eos_token_id=tokenizer.eos_token_id,
        pad_token_id=tokenizer.bos_token_id,
        num_return_sequences=20, # set to desired number of batch sequences to be generated in parallel
    )

sequences = tokenizer.batch_decode(output_ids, skip_special_tokens=True)

for sequence in sequences:
    print(sequence)

Downstream Use

The model may be fine-tuned or incorporated into protein design workflows, including family-specific generation, protein variant generation, and computational screening pipelines.

Out-of-Scope Use

The model should not be used as the sole basis for experimental, clinical, environmental, or safety-critical decisions. Generated proteins require downstream computational and experimental validation. The model is not guaranteed to generate functional, soluble, safe, or synthesizable proteins.

Bias, Risks, and Limitations

ProtGPT3-1.3B learns from public protein sequence datasets and may reproduce biases present in those datasets. Generated sequences may be low-complexity, nonfunctional, unstable, insoluble, or biologically implausible. Protein generation models may also present dual-use risks if used irresponsibly.

Recommendations

Users should apply appropriate computational filters, expert review, and experimental validation before using generated sequences. Users should also consider responsible-use practices for generative protein design.

Technical Specifications

Model Architecture and Objective

ProtGPT3-1.3B is a decoder-only causal language model using a Mixtral-style sparse Mixture-of-Experts architecture. It was trained with a causal language modeling objective on protein sequences.

Citation

BibTeX:

bibtex

@article{garibbo2026protgpt3,
  title={ProtGPT3: an Open-source family of Promptable and Aligned Protein Language Models},
  author={Garibbo, Michele and Boxo Corominas, Gerard and Stocco, Filippo and Illanes Vicioso, Ramiro and Middendorf, Lasse and Ferruz, Noelia},
  journal={bioRxiv},
  pages={2026--06},
  year={2026},
  publisher={Cold Spring Harbor Laboratory}
}

More Information

All models and code are released through the Hugging Face ecosystem and accompanying code repository.