Peptide Property Prediction ML Frameworks

Tools for predicting biochemical, biophysical, and functional properties of peptides using machine learning. Does NOT include general protein structure prediction, mass spectrometry data processing, or peptide sequence generation/design.

There are 61 peptide property prediction frameworks tracked. 6 score above 50 (established tier). The highest-rated is CompOmics/DeepLC at 68/100 with 75 stars and 1,934 monthly downloads.

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#	Framework	Score	Tier	Stars	Language
1	CompOmics/DeepLC DeepLC: Retention time prediction for peptides carrying any modification.	68	Established	75	Python
2	BojarLab/glycowork Package for processing and analyzing glycans and their role in biology.	60	Established	86	Jupyter Notebook
3	wilhelm-lab/dlomix Python framework for Deep Learning in Proteomics	59	Established	39	Jupyter Notebook
4	BojarLab/CandyCrunch Predicting glycan structure from LC-MS/MS data	57	Established	34	Jupyter Notebook
5	MannLabs/alphapeptdeep Deep learning framework for proteomics	51	Established	146	Jupyter Notebook
6	sidhomj/DeepTCR Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data	51	Established	122	Jupyter Notebook
7	wilhelm-lab/koina Democratizing ML in proteomics	49	Emerging	52	Jupyter Notebook
8	wfondrie/depthcharge A deep learning toolkit for mass spectrometry	48	Emerging	87	Python
9	KrishnaswamyLab/ImmunoStruct [Nature Machine Intelligence] ImmunoStruct enables multimodal deep learning...	45	Emerging	43	Python
10	Noble-Lab/Carafe High quality in silico spectral library generation for data-independent...	43	Emerging	16	Java
11	EttoreRocchi/ResPredAI Implementation of the pipeline described in the work "Artificial...	41	Emerging	5	Python
12	mnielLab/NetTCR-2.2 Sequence-based prediction of peptide-TCR interactions using paired chain data	40	Emerging	13	Python
13	ProteomicsML/ProteomicsML Community-curated tutorials and datasets for ML in proteomics	39	Emerging	58	Jupyter Notebook
14	jiangdada1221/TCRpeg Deep autoregressive generative models capture the intrinsics embedded in...	38	Emerging	8	Jupyter Notebook
15	caranathunge/promor A comprehensive R package for label-free proteomics data analysis and modeling	36	Emerging	16	R
16	akiyamalab/cycpeptmp Implementation of CycPeptMP, an accurate and efficient model for predicting...	35	Emerging	28	Python
17	EttoreRocchi/MaldiAMRKit Comprehensive toolkit for MALDI-TOF mass spectrometry data preprocessing for...	35	Emerging	2	Jupyter Notebook
18	dzjxzyd/UniDL4BioPep webserver	35	Emerging	28	Jupyter Notebook
19	PaccMann/TITAN Code for "T Cell Receptor Specificity Prediction with Bimodal Attention...	34	Emerging	30	Jupyter Notebook
20	scikit-fingerprints/peptides_molecular_fingerprints_classification Code for paper "Molecular Fingerprints Are Strong Models for Peptide...	34	Emerging	4	Jupyter Notebook
21	Martinaa1408/LB2_project_Group_5 This repository contains the datasets, scripts, and analyses for the...	32	Emerging	3	Jupyter Notebook
22	BojarLab/SweetNet Graph convolutional neural networks for analyzing glycans [LEGACY; use...	31	Emerging	17	Jupyter Notebook
23	raghavagps/toxinpred2 An improved method for predicting toxicity of proteins	31	Emerging	18	Perl
24	Protein-Engineering-Framework/PyPEF PyPEF – Pythonic Protein Engineering Framework	31	Emerging	25	Python
25	FennOmix/FennOmix.MHC Foundation model for MHC class I peptide binding prediction built on deep...	30	Emerging	5	Python
26	MannLabs/PeptDeep-HLA DL model to predict HLA peptide presentation	30	Emerging	16	Jupyter Notebook
27	EMSL-Computing/PeakDecoder A workflow for metabolite identification and accurate profiling in...	30	Emerging	16	R
28	BojarLab/LectinOracle Deep learning model to predict interactions between proteins and glycans...	29	Experimental	14	Jupyter Notebook
29	wilhelm-lab/PROSPECT Proteomics Mass Spectrometry Datasets for Machine Learning	29	Experimental	22	Python
30	pengxingang/TEIM TEIM: TCR-Epitope Interaction Modeling	29	Experimental	56	Python
31	Wishartlab-openscience/Biotransformer A computational tool for the prediction and identification of metabolites.	27	Experimental	10	Java
32	raghavagps/hemopi2 HemoPI2: Prediction of hemolytic activity of peptides against mammalian RBCs	27	Experimental	13	Python
33	M-Serajian/MTB-Pipeline MTB++ a software developed to predict antimicrobial resistance to 13...	26	Experimental	3	Python
34	kalininalab/ALPAR Single Reference Antimicrobial Resistance	26	Experimental	7	Python
35	kbcoulter/deep_metab Applying Deep Learning Methods to LC-MS Metabolomics Data to Improve...	26	Experimental	6	Python
36	nec-research/tc-hard Experiments for "On TCR Binding Predictors Failing to Generalize to Unseen...	26	Experimental	8	Jupyter Notebook
37	lkytal/PepNet The state of the art Deep CNN neural network for de novo sequencing of...	26	Experimental	39	Python
38	bigict/ProTCR Predicting neoantigen and T-cell receptor binding by integrating structural...	25	Experimental	2	Python
39	HolobiomicsLab/MetaboT 🤖 MetaboT 🍵 is an AI system that accelerates mass spectrometry-based...	25	Experimental	25	Jupyter Notebook
40	molML/peptidy The official codebase of peptidy, a peptide processing tool for machine learning.	24	Experimental	36	Python
41	BioGenies/peptide-prediction-list Collects software dedicated to predicting specific properties of peptides	23	Experimental	68	Shell
42	Rishu-raj-02/AMR-Multi-Antibiotic-Resistance-Predictor 🧬 AI-powered multi-task model predicting E. coli resistance to...	22	Experimental	—	HTML
43	dan-veltri/amp-scanner-v2 Antimicrobial Peptide Scanner Version 2. Open source GLPv3 release of code...	22	Experimental	9	Python
44	XSLiuLab/TLimmuno2 TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning	22	Experimental	12	HTML
45	JRaviLab/amRml Houses the AMR ML and post-ML package	22	Experimental	—	R
46	sablokrep/amnz antimicrobial machine learning	22	Experimental	—	Rust
47	hcji/AutoMS Deep Denoising Autoencoder-assisted Continuous Scoring of Peak Quality in...	22	Experimental	7	Jupyter Notebook
48	Ardit-Mishra/peptide-mhc-binding-predictor A full-stack computational immunology research interface for exploring...	19	Experimental	—	TypeScript
49	faezesarlakifar/AllerTrans A Deep Learning Method for Predicting the Allergenicity of Protein Sequences	19	Experimental	6	Jupyter Notebook
50	unumbrela/amp-research2 AMP generation research report with model comparison, evaluation methods,...	14	Experimental	—	TypeScript
51	PedroSeber/O-GlcNAcylation_Prediction Code and datasets for the publications "Predicting O-GlcNAcylation sites in...	14	Experimental	3	Python
52	AlBadruSsenoga/gritapamr Machine learning (ML) models using sourced data (Antimicrobial Testing...	14	Experimental	—	Jupyter Notebook
53	NasirNesirli/kleb-amr-project Interpretable Deep-Learning and Ensemble Models for Predicting Multidrug...	14	Experimental	—	HTML
54	nesirli/msc-project Interpretable Deep-Learning and Ensemble Models for Predicting Multidrug...	14	Experimental	—	HTML
55	Peldom/Peplib_Generator The one model for genesis of peptide ligands	13	Experimental	8	—
56	AstraBert/resistML A tool for AMR gene family prediction, simple and ML-based	12	Experimental	4	Jupyter Notebook
57	a-avasilenko/Proteomics-multivariate-analysis Multivariate analysis of proteomics data comparing PCA and LASSO with...	11	Experimental	—	Jupyter Notebook
58	ksuee108/MO_AMP_Designer This Streamlit app is designed to facilitate the de novo design of...	11	Experimental	—	Python
59	PedroSeber/CHO_N-glycosylation_prediction Code and datasets for the publication "Linear and Neural Network Models for...	11	Experimental	2	Jupyter Notebook
60	panos-gbio/Proteomics-in-Latent-Space Repository for my MSc thesis project in Scilifelab - Proteoform Networks...	11	Experimental	—	Jupyter Notebook
61	musfiquejim/EnACP-A-Hybrid-Machine-Learning-Framework-for-Detecting-Anticancer-Peptides EnACP: একটি Ensemble Learning মডেল যা অ্যান্টিক্যান্সার পেপটাইড সনাক্তকরণের...	10	Experimental	1	Shell

Comparisons in this category

DeepTCR and TCRpeg (51 vs 38)