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 36 protein transformers ml models tracked. The highest-rated is lucidrains/alphagenome at 49/100 with 97 stars.

Get all 36 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	49	Emerging	97	Jupyter Notebook
2	BiomedSciAI/biomed-multi-omic Build foundation model for RNA or DNA data	48	Emerging	56	Jupyter Notebook
3	BioinfoMachineLearning/DeepInteract A geometric deep learning framework (Geometric Transformers) for predicting...	46	Emerging	64	Python
4	Gleghorn-Lab/Protify Low code molecular property prediction	43	Emerging	11	Python
5	raimondilab/precogx A predictor of GPCR couplings with G-proteins/B-arrs using Transformers	41	Emerging	10	JavaScript
6	ziegler-ingo/cleavage_benchmark [BIBM 2025] Code and resources for the paper "Enhancing Multi-Epitope...	37	Emerging	6	Python
7	Bindwell/PLAPT Codebase and CLI for PLAPT: A state-of-the-art protein-ligand binding...	33	Emerging	114	Mathematica
8	BoHuangLab/Protein-Localization-Transformer Code for CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein...	28	Experimental	29	Python
9	SkywalkerLuke/TransHLA TransHLA: A hybrid transformer model for peptide-HLA epitope detection.	28	Experimental	9	Python
10	yotamnahum/DNA-Data-Storage Single Read Reconstruction for DNA Data Storage Using Transformers (official...	26	Experimental	5	Python
11	AspirinCode/AlphaPPImd Exploring the conformational ensembles of protein-protein complexes with...	25	Experimental	33	Jupyter Notebook
12	KCLabMTU/LMCrot Protein Language Model (pLM) Powered Protein Crotonylation (Kcr) Modified...	25	Experimental	4	Python
13	BoHuangLab/CELL-E_2 Multimodal encoder-only transformer model for image-based protein predictions	25	Experimental	15	Python
14	debugst1ck/tarp 🦠 Antimicrobial resistance prediction using transformer models.	24	Experimental	2	Jupyter Notebook
15	En1gma02/Proteomic-and-Genomic-Drug-Development An end-to-end generative AI pipeline for Proteomic and Genomic drug...	24	Experimental	2	Jupyter Notebook
16	DrHB/rna-stanford Transformer + GAT for RNA chemical reactivity prediction\| Stanford Ribonanza	23	Experimental	11	Jupyter Notebook
17	Pranavgosavi217/Kaggle-RNA-3D 🧬 Predict RNA 3D structures with an interactive dashboard and reusable...	22	Experimental	—	Python
18	MachineLearningLifeScience/awesome-protein-foundation-models A curated list of protein foundation models, protein language models (pLMs),...	22	Experimental	—	—
19	geneexpressionpolito/Predicting-gene-expression-levels-from-DNA-sequences-and-post-transcriptional-info-with-transformers Transformers for gene expression prediction from raw dna sequences	22	Experimental	16	Jupyter Notebook
20	USask-BINFO/AcrTransAct Implementation of the paper "AcrTransAct: Pre-trained Protein Transformer...	22	Experimental	1	Python
21	sermare/DeepOff Deep Learning to predict phenotype score associated with heritable gene...	22	Experimental	1	Jupyter Notebook
22	Ankit6174/Domain-Specific-Mini-LLM-for-Genomic-Mutation-Prediction An encoder only transformer model that accurately predicts the type, genomic...	20	Experimental	1	Jupyter Notebook
23	ByteAlchemyModels/protein-ml Multi-phase peptide ML pipeline for hemolysis prediction, generative design,...	19	Experimental	—	Python
24	firebitsbr/Stanford-RNA-3D-Folding This repository contains a comprehensive solution for the Stanford RNA 3D...	17	Experimental	2	Jupyter Notebook
25	nnilayy/BioCore A comprehensive bioinformatics platform/suite for molecular biology research...	17	Experimental	2	Jupyter Notebook
26	ewijaya/protein-lm-distill Compact protein language models via knowledge distillation from ProtGPT2....	16	Experimental	2	Python
27	Lwg78/genomic-decoder-v2 End-to-end Transformer model for Drosophila DNA decoding.	15	Experimental	—	Jupyter Notebook
28	vkhamesi/proteins 🧬 Fine-Tuning Large Language and Protein Models on a single T4 GPU via...	14	Experimental	7	Jupyter Notebook
29	Bhattacharya-Lab/CASP15 CASP15 performance benchmarking of the state-of-the-art protein structure...	14	Experimental	12	—
30	shalakapadalkar16/viral-genome-classifier Production-ready ML pipeline for viral genome classification from NCBI...	13	Experimental	—	Python
31	MuthusaravananS/PINPOINT Pipeline for discovering novel protease inhibtiors at plant pathogen interface.	12	Experimental	1	Jupyter Notebook
32	azwad-tamir/Prot_EC A Transformer Based Deep Learning System for Accurate Annotation of Enzyme...	12	Experimental	1	Python
33	rouni001/Simulated-Genomic-Sequence-Generator Simulated Genomic Sequence Generator using Self-Supervised Learning Architectures	12	Experimental	1	Python
34	zelenkastiot/s-gene-mutations-SARS-CoV-2 Processing GISAID SARS-CoV-2 emerging variants data and generating a...	12	Experimental	4	Jupyter Notebook
35	baksho/AMRxformer Predict antomicrobial resistance (AMR) for a pathogen (Staphylococcus...	11	Experimental	—	Jupyter Notebook
36	lily98b/ProteinEvolution Combining NLP models and genetic algorithms for high-pLDDT protein sequence design.	11	Experimental	—	Python