Protein Transformers ML Transformer Models

Tools for applying transformer models to protein-related tasks including structure prediction, function prediction, binding/interaction analysis, and protein design. Does NOT include general protein analysis tools, genomic/DNA sequence analysis, or non-transformer-based bioinformatics methods.

There are 37 protein transformers ml models tracked. 3 score above 50 (established tier). The highest-rated is lucidrains/alphagenome at 55/100 with 97 stars.

Get all 37 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=transformers&subcategory=protein-transformers-ml&limit=20"

Open to everyone — 100 requests/day, no key needed. Get a free key for 1,000/day.

#	Model	Score	Tier	Stars	Language
1	lucidrains/alphagenome Implementation of AlphaGenome, Deepmind's updated genomic attention model	55	Established	97	Jupyter Notebook
2	BiomedSciAI/biomed-multi-omic Build foundation model for RNA or DNA data	52	Established	56	Jupyter Notebook
3	BioinfoMachineLearning/DeepInteract A geometric deep learning framework (Geometric Transformers) for predicting...	50	Established	64	Python
4	Gleghorn-Lab/Protify Low code molecular property prediction	47	Emerging	11	Python
5	raimondilab/precogx A predictor of GPCR couplings with G-proteins/B-arrs using Transformers	45	Emerging	10	JavaScript
6	ziegler-ingo/cleavage_benchmark [BIBM 2025] Code and resources for the paper "Enhancing Multi-Epitope...	44	Emerging	6	Python
7	Bindwell/PLAPT Codebase and CLI for PLAPT: A state-of-the-art protein-ligand binding...	40	Emerging	114	Mathematica
8	BoHuangLab/Protein-Localization-Transformer Code for CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein...	35	Emerging	29	Python
9	SkywalkerLuke/TransHLA TransHLA: A hybrid transformer model for peptide-HLA epitope detection.	35	Emerging	9	Python
10	yotamnahum/DNA-Data-Storage Single Read Reconstruction for DNA Data Storage Using Transformers (official...	33	Emerging	5	Python
11	KCLabMTU/LMCrot Protein Language Model (pLM) Powered Protein Crotonylation (Kcr) Modified...	32	Emerging	4	Python
12	BoHuangLab/CELL-E_2 Multimodal encoder-only transformer model for image-based protein predictions	32	Emerging	15	Python
13	AspirinCode/AlphaPPImd Exploring the conformational ensembles of protein-protein complexes with...	32	Emerging	33	Jupyter Notebook
14	DrHB/rna-stanford Transformer + GAT for RNA chemical reactivity prediction\| Stanford Ribonanza	30	Emerging	11	Jupyter Notebook
15	sermare/DeepOff Deep Learning to predict phenotype score associated with heritable gene...	29	Experimental	1	Jupyter Notebook
16	USask-BINFO/AcrTransAct Implementation of the paper "AcrTransAct: Pre-trained Protein Transformer...	29	Experimental	1	Python
17	geneexpressionpolito/Predicting-gene-expression-levels-from-DNA-sequences-and-post-transcriptional-info-with-transformers Transformers for gene expression prediction from raw dna sequences	29	Experimental	16	Jupyter Notebook
18	debugst1ck/tarp 🦠 Antimicrobial resistance prediction using transformer models.	27	Experimental	2	Jupyter Notebook
19	Ankit6174/Domain-Specific-Mini-LLM-for-Genomic-Mutation-Prediction An encoder only transformer model that accurately predicts the type, genomic...	26	Experimental	1	Jupyter Notebook
20	nnilayy/BioCore A comprehensive bioinformatics platform/suite for molecular biology research...	24	Experimental	2	Jupyter Notebook
21	MachineLearningLifeScience/awesome-protein-foundation-models A curated list of protein foundation models, protein language models (pLMs),...	21	Experimental	—	—
22	ByteAlchemyModels/protein-ml Multi-phase peptide ML pipeline for hemolysis prediction, generative design,...	21	Experimental	—	Python
23	vkhamesi/proteins 🧬 Fine-Tuning Large Language and Protein Models on a single T4 GPU via...	21	Experimental	7	Jupyter Notebook
24	Bhattacharya-Lab/CASP15 CASP15 performance benchmarking of the state-of-the-art protein structure...	21	Experimental	12	—
25	rouni001/Simulated-Genomic-Sequence-Generator Simulated Genomic Sequence Generator using Self-Supervised Learning Architectures	19	Experimental	1	Python
26	zelenkastiot/s-gene-mutations-SARS-CoV-2 Processing GISAID SARS-CoV-2 emerging variants data and generating a...	19	Experimental	4	Jupyter Notebook
27	azwad-tamir/Prot_EC A Transformer Based Deep Learning System for Accurate Annotation of Enzyme...	19	Experimental	1	Python
28	Lwg78/genomic-decoder-v2 End-to-end Transformer model for Drosophila DNA decoding.	17	Experimental	—	Jupyter Notebook
29	ewijaya/protein-lm-distill Compact protein language models via knowledge distillation from ProtGPT2....	17	Experimental	2	Python
30	shalakapadalkar16/viral-genome-classifier Production-ready ML pipeline for viral genome classification from NCBI...	15	Experimental	—	Python
31	MuthusaravananS/PINPOINT Pipeline for discovering novel protease inhibtiors at plant pathogen interface.	14	Experimental	1	Jupyter Notebook
32	baksho/AMRxformer Predict antomicrobial resistance (AMR) for a pathogen (Staphylococcus...	13	Experimental	—	Jupyter Notebook
33	lily98b/ProteinEvolution Combining NLP models and genetic algorithms for high-pLDDT protein sequence design.	13	Experimental	—	Python
34	dacarlin/protein-transformers Use generative ML to design new proteins using this simple, hackable...	13	Experimental	9	Python
35	ziegler-ingo/cleavage_prediction Code and dataset for the NeurIPS'22 paper "What cleaves? Is proteasomal...	12	Experimental	5	Jupyter Notebook
36	dohlee/proteinbert-pytorch Implementation of ProteinBERT, a deep language model designed for proteins.	11	Experimental	3	Python
37	ginevracoal/adversarial-protein-sequences Code for paper "Adversarial Attacks on Protein Language Models", Ginevra...	10	Experimental	2	Python