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maraxen/
prxteinmpnn

structure-based-design

mit

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[!WARNING] This repository is archived and no longer maintained.

All weights have been migrated to maraxen/aminx, which covers ProteinMPNN, SolubleMPNN, LigandMPNN, Membrane variants, and the side-chain packer — all in the compressed .eqx.zst format with parity-verified conversions.

Install the new package:

pip install aminx # weights auto-download from maraxen/aminx on first use

PrxteinMPNN (archived)

A JAX/Equinox implementation of ProteinMPNN for inverse protein folding and sequence design.

Model Description

PrxteinMPNN is a message-passing neural network that generates amino acid sequences given a protein backbone structure. This implementation uses JAX and Equinox for efficient computation and functional programming patterns.

Key Features:

Fully modular Equinox implementation
JAX-based for GPU acceleration and automatic differentiation
Multiple pre-trained model variants (original and soluble)
Multiple training epochs (002, 010, 020, 030)

Available Models

All models use the same architecture with different training:

Original Models

original_v_48_002 - Trained for 2 epochs
original_v_48_010 - Trained for 10 epochs
original_v_48_020 - Trained for 20 epochs (recommended)
original_v_48_030 - Trained for 30 epochs

Soluble Models

soluble_v_48_002 - Trained for 2 epochs on soluble proteins
soluble_v_48_010 - Trained for 10 epochs on soluble proteins
soluble_v_48_020 - Trained for 20 epochs on soluble proteins (recommended)
soluble_v_48_030 - Trained for 30 epochs on soluble proteins

Installation

pip install jax equinox huggingface_hub

Usage

Basic Usage

python

import jax
import jax.numpy as jnp
import equinox as eqx
from huggingface_hub import hf_hub_download

# Download model from HuggingFace
model_path = hf_hub_download(
    repo_id="maraxen/prxteinmpnn",
    filename="eqx/original_v_48_020.eqx",
    repo_type="model",
)

# Create model structure (must match saved architecture)
from prxteinmpnn.eqx_new import PrxteinMPNN

key = jax.random.PRNGKey(0)
model = PrxteinMPNN(
    node_features=128,
    edge_features=128,
    hidden_features=512,
    num_encoder_layers=3,
    num_decoder_layers=3,
    vocab_size=21,
    k_neighbors=48,
    key=key,
)

# Load weights
model = eqx.tree_deserialise_leaves(model_path, model)

# Use model for inference
# ... (see full documentation for inference examples)

Using the New Package (Recommended)

python

from aminx.io.weights import load_model

# Automatically downloads and loads the model from maraxen/aminx
model = load_model("proteinmpnn_v_48_020")

Model Architecture

Hyperparameters:

Node features: 128
Edge features: 128
Hidden features: 512
Encoder layers: 3
Decoder layers: 3
K-nearest neighbors: 48
Vocabulary size: 21 (20 amino acids + 1 unknown)

Architecture:

Message-passing encoder for structural features
Autoregressive decoder for sequence generation
Attention-based edge updates
LayerNorm and residual connections

Citation

If you use PrxteinMPNN in your research, please cite the original ProteinMPNN paper:

bibtex

@article{dauparas2022robust,
  title={Robust deep learning--based protein sequence design using ProteinMPNN},
  author={Dauparas, Justas and Anishchenko, Ivan and Bennett, Nathaniel and Bai, Hua and Ragotte, Robert J and Milles, Lukas F and Wicky, Basile IM and Courbet, Alexis and de Haas, Rob J and Bethel, Neville and others},
  journal={Science},
  volume={378},
  number={6615},
  pages={49--56},
  year={2022},
  publisher={American Association for the Advancement of Science}
}

License

MIT License - See LICENSE file for details.

maraxen/prxteinmpnn