Protein Language Models ML Frameworks

Tools for training and applying transformer-based language models on protein sequences for tasks like fitness prediction, stability estimation, and property inference. Does NOT include structure prediction, sequence alignment, or general protein embeddings without generative/discriminative language modeling.

There are 55 protein language models frameworks tracked. 3 score above 50 (established tier). The highest-rated is DeepRank/deeprank2 at 62/100 with 57 stars and 114 monthly downloads.

Get all 55 projects as JSON

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

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#	Framework	Score	Tier	Stars	Language
1	DeepRank/deeprank2 An open-source deep learning framework for data mining of protein-protein...	62	Established	57	Python
2	sacdallago/biotrainer Biological prediction models made simple.	58	Established	49	Python
3	jonathanking/sidechainnet An all-atom protein structure dataset for machine learning.	51	Established	360	Python
4	a-r-j/ProteinWorkshop Benchmarking framework for protein representation learning. Includes a large...	48	Emerging	268	Python
5	BioinfoMachineLearning/DIPS-Plus The Enhanced Database of Interacting Protein Structures for Interface Prediction	46	Emerging	54	Python
6	idrblab/AnnoPRO Feature map and function annotation of Proteins	45	Emerging	34	Python
7	songlab-cal/tape Tasks Assessing Protein Embeddings (TAPE), a set of five biologically...	43	Emerging	733	Python
8	flatironinstitute/DeepFRI Deep functional residue identification	42	Emerging	348	Python
9	aqlaboratory/proteinnet Standardized data set for machine learning of protein structure	42	Emerging	910	Python
10	jaswindersingh2/SPOT-RNA RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep...	41	Emerging	107	Perl
11	LBM-EPFL/PeSTo Geometric deep learning method to predict protein binding interfaces from a...	37	Emerging	156	Jupyter Notebook
12	jonathanking/protein-transformer Predicting protein structure through sequence modeling	35	Emerging	112	Jupyter Notebook
13	michaelhla/pro-1 reasoning model trained using GRPO towards rosetta REF2015 for protein stability	35	Emerging	101	Python
14	HannesStark/protein-localization Using Transformer protein embeddings with a linear attention mechanism to...	34	Emerging	76	Jupyter Notebook
15	anton-bushuiev/PPIformer Learning to design protein-protein interactions with enhanced generalization...	33	Emerging	53	Jupyter Notebook
16	vsomnath/holoprot Multi-Scale Representation Learning on Proteins (NeurIPS 2021)	33	Emerging	49	Python
17	anton-bushuiev/PPIRef Dataset and package for working with protein-protein interactions in 3D	31	Emerging	105	Jupyter Notebook
18	dohlee/abyssal-pytorch Implementation of Abyssal, a deep neural network trained with a new "mega"...	31	Emerging	6	Jupyter Notebook
19	adaptyvbio/ProteinFlow Versatile computational pipeline for processing protein structure data for...	31	Emerging	274	Python
20	aws-samples/lm-gvp LM-GVP: A Generalizable Deep Learning Framework for Protein Property...	30	Emerging	65	Jupyter Notebook
21	victor369basu/ProteinStructurePrediction Protein structure prediction is the task of predicting the 3-dimensional...	30	Emerging	20	Python
22	vam-sin/CATHe Deep Learning tool trained on protein sequence embeddings from protein...	30	Emerging	15	Python
23	OpenProteinAI/PoET Inference code for PoET: A generative model of protein families as...	28	Experimental	93	Python
24	conradry/prtm Deep learning for protein science	28	Experimental	38	Python
25	lightonai/RITA RITA is a family of autoregressive protein models, developed by LightOn in...	28	Experimental	98	Python
26	dohlee/rasp-pytorch Reimplementation of RaSP, a deep neural network for rapid protein stability...	28	Experimental	4	Python
27	draeger-lab/TFpredict Identification and structural characterization of transcription factors...	27	Experimental	7	Java
28	QizhiPei/BioT5 BioT5 (EMNLP 2023) and BioT5+ (ACL 2024 Findings)	27	Experimental	123	Python
29	bioinfodlsu/phage-host-prediction Published in PLOS ONE. Phage-host interaction prediction tool that uses...	26	Experimental	17	Jupyter Notebook
30	MachineLearningLifeScience/protein_regression The codebase to replicate the analysis of "A systematic analysis of...	26	Experimental	5	Jupyter Notebook
31	Bitbol-Lab/DiffPALM Differentiable Pairing using Alignment-based Language Models	25	Experimental	24	Jupyter Notebook
32	milagjurovska/PPI-link-prediction-with-optimized-gcn-and-gan Comparing different biologically inspired algorithms in hyperparameter...	24	Experimental	2	Python
33	google-research/slip SLIP is a sandbox environment for engineering protein sequences with...	24	Experimental	21	Python
34	NIGMS/Protein-Protein-Interactions-using-ML In this module, you will harness novel machine learning techniques to...	24	Experimental	—	Jupyter Notebook
35	jiaqingxie/DeepProtein Deep Learning Library and Benchmark for Protein Sequence Learning...	23	Experimental	41	Jupyter Notebook
36	JieZheng-ShanghaiTech/SL_benchmark Benchmarking study of machine learning methods for prediction of synthetic lethality	23	Experimental	19	Python
37	kiwijuice56/protein-visualizer Visualizing the function of biological proteins through deep learning. MIT...	22	Experimental	7	Python
38	jsmccabe1/ApiPred Predict fitness phenotypes and invasion machinery in apicomplexan parasites...	22	Experimental	—	Python
39	bschilder/VEP_protein Using Protein Language Models to compute Variant Effect Predictions across...	22	Experimental	—	Jupyter Notebook
40	Ulton321/Protein-Language-Model-Steering Protein-Language-Model-Steering explores how to guide or "steer" large...	22	Experimental	3	Jupyter Notebook
41	raphamontana/BioNCE An Intelligent digital system for classification of molecules querying...	22	Experimental	1	JavaScript
42	jgbrasier/protein-classification Deep sequence models for protein classification	21	Experimental	9	Jupyter Notebook
43	daisybio/data-leakage-ppi-prediction Code associated with the paper 'Cracking the blackbox of deep sequence-based...	20	Experimental	27	C++
44	omarperacha/ps4-dataset The largest open-source dataset for Protein Single Sequence Secondary...	20	Experimental	14	Python
45	shruti-sivakumar/MSA-Comparative-Study Benchmarking 6 MSA tools (Clustal Omega, MUSCLE, MAGUS, M-Coffee, MSA Probs,...	19	Experimental	—	—
46	310-ai/lib310 lib310 python package	18	Experimental	23	C++
47	DeepFoldProtein/OTalign OTalign: Protein sequence alignment for remote homologs using Protein...	17	Experimental	3	Python
48	claopodium/SLP-for-Bio Based on Single Layer Perceptron model, the programme intended to locate key...	16	Experimental	2	Python
49	bioinfodlsu/PHIStruct Published in Bioinformatics. Phage-host interaction prediction tool that...	16	Experimental	9	Jupyter Notebook
50	allamiro/9mers-structure-prediction Protein structure prediction for CullPDB 9-mer fragments using multi-input...	15	Experimental	—	—
51	MPI-Dortmund/pymissense PyMissense creates the pathogenicity plot and modified pdb as shown in the...	15	Experimental	23	Python
52	A-Hareed/BackMapNet BackMapNet is a deep-learning framework for reconstructing all-atom protein...	14	Experimental	—	Python
53	mciaravino/yeast-protein-classification Multiclass classification of yeast protein localization sites using multiple...	14	Experimental	—	Jupyter Notebook
54	kren-ai-lab/RUDEUS Developing classification models for DNA-Binding proteins through machine...	12	Experimental	4	Jupyter Notebook
55	phenolophthaleinum/phastDNA Virus-host interaction prediction using local fluctuations of genome...	12	Experimental	3	HTML