Protein Language Model Python Packages

atlasfold

Trainable protein folding and co-folding models with a protein language model.

bionemo-ir

Easy, fast, and memory-efficient structure prediction inference

biocentral-api

Programmatic access to the biocentral ecosystem.

sceptr

Highly informative TCR representation model

biocentral

Biomedical data, from lab to paper.

abyssal-pytorch

Implementation of Abyssal, a deep neural network trained with a new "mega" dataset to predict the impact of an amino acid variant on protein stability.

esmc-protein-function

An Evolutionary-scale Model (ESM) for protein function prediction from amino acid sequences using the Gene Ontology (GO).

prime-metal

Implementation of PRIME: Probe-Based Identification of Metal-Binding Sites Using Deep Learning Representations

esmc-function-classifier

An Evolutionary-scale Model (ESM) for protein function prediction from amino acid sequences using the Gene Ontology (GO).

proteintensor

AI-native tensor format (.ptt) for structural biology ML. Convert a protein/nucleic-acid/ligand structure or sequence once; load backbone, MSA, ESM embeddings, sparse pair features, and ligand pockets with zero parsing. Feeds Boltz-2 (verified), AlphaFold 3, Chai-1, Nesso. Zarr-backed, PyTorch/JAX, streams from S3/GCS.

ablanx

JAX/Flax port of AbLang2's AbRep encoder: differentiable antibody language-model embeddings and per-block attention, loading the original weights unchanged.

protflash

ProtFlash: A lightweight protein language model

protembedder

Extract protein embeddings from FASTA files using ESM-2, ProtT5, and ProtBert models

spectrae

SPECTRA: Spectral framework for evaluation of biomedical AI models

protlib-designer

Design diverse, optimized protein libraries with multi-objective integer programming, deep mutational scanning, protein language models, and inverse folding.

antiberty-pytorch

An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.

deepab-pytorch

An unofficial re-implementation of DeepAb, an interpretable deep learning model for antibody structure prediction.

proteinbert-pytorch-reproduction

Implementation of ProteinBERT, a deep language model designed for proteins.