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 60 protein language models frameworks tracked. 6 score above 50 (established tier). The highest-rated is DeepRank/deeprank2 at 61/100 with 57 stars.

Get all 60 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...	61	Established	57	Python
2	sacdallago/biotrainer Biological prediction models made simple.	60	Established	49	Python
3	jonathanking/sidechainnet An all-atom protein structure dataset for machine learning.	52	Established	360	Python
4	a-r-j/ProteinWorkshop Benchmarking framework for protein representation learning. Includes a large...	50	Established	268	Python
5	songlab-cal/tape Tasks Assessing Protein Embeddings (TAPE), a set of five biologically...	50	Established	733	Python
6	BioinfoMachineLearning/DIPS-Plus The Enhanced Database of Interacting Protein Structures for Interface Prediction	50	Established	54	Python
7	flatironinstitute/DeepFRI Deep functional residue identification	49	Emerging	348	Python
8	aqlaboratory/proteinnet Standardized data set for machine learning of protein structure	49	Emerging	910	Python
9	idrblab/AnnoPRO Feature map and function annotation of Proteins	48	Emerging	34	Python
10	jaswindersingh2/SPOT-RNA RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep...	48	Emerging	107	Perl
11	LBM-EPFL/PeSTo Geometric deep learning method to predict protein binding interfaces from a...	44	Emerging	156	Jupyter Notebook
12	jonathanking/protein-transformer Predicting protein structure through sequence modeling	42	Emerging	112	Jupyter Notebook
13	michaelhla/pro-1 reasoning model trained using GRPO towards rosetta REF2015 for protein stability	42	Emerging	101	Python
14	HannesStark/protein-localization Using Transformer protein embeddings with a linear attention mechanism to...	41	Emerging	76	Jupyter Notebook
15	vsomnath/holoprot Multi-Scale Representation Learning on Proteins (NeurIPS 2021)	40	Emerging	49	Python
16	anton-bushuiev/PPIformer Learning to design protein-protein interactions with enhanced generalization...	40	Emerging	53	Jupyter Notebook
17	adaptyvbio/ProteinFlow Versatile computational pipeline for processing protein structure data for...	38	Emerging	274	Python
18	anton-bushuiev/PPIRef Dataset and package for working with protein-protein interactions in 3D	38	Emerging	105	Jupyter Notebook
19	aws-samples/lm-gvp LM-GVP: A Generalizable Deep Learning Framework for Protein Property...	37	Emerging	65	Jupyter Notebook
20	victor369basu/ProteinStructurePrediction Protein structure prediction is the task of predicting the 3-dimensional...	37	Emerging	20	Python
21	vam-sin/CATHe Deep Learning tool trained on protein sequence embeddings from protein...	37	Emerging	15	Python
22	conradry/prtm Deep learning for protein science	35	Emerging	38	Python
23	lightonai/RITA RITA is a family of autoregressive protein models, developed by LightOn in...	35	Emerging	98	Python
24	OpenProteinAI/PoET Inference code for PoET: A generative model of protein families as...	35	Emerging	93	Python
25	dohlee/abyssal-pytorch Implementation of Abyssal, a deep neural network trained with a new "mega"...	34	Emerging	6	Jupyter Notebook
26	QizhiPei/BioT5 BioT5 (EMNLP 2023) and BioT5+ (ACL 2024 Findings)	34	Emerging	123	Python
27	draeger-lab/TFpredict Identification and structural characterization of transcription factors...	34	Emerging	7	Java
28	MachineLearningLifeScience/protein_regression The codebase to replicate the analysis of "A systematic analysis of...	33	Emerging	5	Jupyter Notebook
29	bioinfodlsu/phage-host-prediction Published in PLOS ONE. Phage-host interaction prediction tool that uses...	33	Emerging	17	Jupyter Notebook
30	dohlee/rasp-pytorch Reimplementation of RaSP, a deep neural network for rapid protein stability...	32	Emerging	4	Python
31	Bitbol-Lab/DiffPALM Differentiable Pairing using Alignment-based Language Models	32	Emerging	24	Jupyter Notebook
32	google-research/slip SLIP is a sandbox environment for engineering protein sequences with...	31	Emerging	21	Python
33	jiaqingxie/DeepProtein Deep Learning Library and Benchmark for Protein Sequence Learning...	30	Emerging	41	Jupyter Notebook
34	milagjurovska/PPI-link-prediction-with-optimized-gcn-and-gan Comparing different biologically inspired algorithms in hyperparameter...	30	Emerging	2	Python
35	JieZheng-ShanghaiTech/SL_benchmark Benchmarking study of machine learning methods for prediction of synthetic lethality	30	Emerging	19	Python
36	kiwijuice56/protein-visualizer Visualizing the function of biological proteins through deep learning. MIT...	29	Experimental	7	Python
37	jgbrasier/protein-classification Deep sequence models for protein classification	28	Experimental	9	Jupyter Notebook
38	daisybio/data-leakage-ppi-prediction Code associated with the paper 'Cracking the blackbox of deep sequence-based...	27	Experimental	27	C++
39	omarperacha/ps4-dataset The largest open-source dataset for Protein Single Sequence Secondary...	27	Experimental	14	Python
40	310-ai/lib310 lib310 python package	25	Experimental	23	C++
41	NIGMS/Protein-Protein-Interactions-using-ML In this module, you will harness novel machine learning techniques to...	24	Experimental	—	Jupyter Notebook
42	Ulton321/Protein-Language-Model-Steering Protein-Language-Model-Steering explores how to guide or "steer" large...	24	Experimental	3	Jupyter Notebook
43	bioinfodlsu/PHIStruct Published in Bioinformatics. Phage-host interaction prediction tool that...	23	Experimental	9	Jupyter Notebook
44	MPI-Dortmund/pymissense PyMissense creates the pathogenicity plot and modified pdb as shown in the...	22	Experimental	23	Python
45	jsmccabe1/ApiPred Predict fitness phenotypes and invasion machinery in apicomplexan parasites...	22	Experimental	—	Python
46	shruti-sivakumar/MSA-Comparative-Study Benchmarking 6 MSA tools (Clustal Omega, MUSCLE, MAGUS, M-Coffee, MSA Probs,...	21	Experimental	—	—
47	DeepFoldProtein/OTalign OTalign: Protein sequence alignment for remote homologs using Protein...	20	Experimental	3	Python
48	kren-ai-lab/RUDEUS Developing classification models for DNA-Binding proteins through machine...	19	Experimental	4	Jupyter Notebook
49	phenolophthaleinum/phastDNA Virus-host interaction prediction using local fluctuations of genome...	19	Experimental	3	HTML
50	claopodium/SLP-for-Bio Based on Single Layer Perceptron model, the programme intended to locate key...	18	Experimental	2	Python
51	allamiro/9mers-structure-prediction Protein structure prediction for CullPDB 9-mer fragments using multi-input...	17	Experimental	—	—
52	A-Hareed/BackMapNet BackMapNet is a deep-learning framework for reconstructing all-atom protein...	14	Experimental	—	Python
53	Faluminus/Sec-PRED Protein secondary structure prediction from amino acid sequence using...	14	Experimental	6	Python
54	mciaravino/yeast-protein-classification Multiclass classification of yeast protein localization sites using multiple...	11	Experimental	—	Jupyter Notebook
55	kalininalab/NaturalPPLuM Repository of the paper "Exploring sequence landscape of biosynthetic gene...	11	Experimental	3	Jupyter Notebook
56	FAhtisham/Protein-Crotonylation The repository contains the codes to predict protein crotonylation, existing...	11	Experimental	—	—
57	DSIMB/PYTHIA Deep Learning Approach For Local Protein Conformation Prediction	11	Experimental	3	Perl
58	dohlee/tranception-pytorch Implementation of Tranception, a SOTA transformer model for protein fitness...	11	Experimental	3	Jupyter Notebook
59	albaaggbb/protein-classification-ann Deep learning approach for multiclass classification of mice based on...	10	Experimental	1	HTML
60	khanovico/neural-struct-detect deep neural network for detecting structure of protein	10	Experimental	2	Python