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 60 peptide property prediction frameworks tracked. 1 score above 70 (verified tier). The highest-rated is CompOmics/DeepLC at 75/100 with 75 stars and 2,012 monthly downloads.

Get all 60 projects as JSON

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#	Framework	Score	Tier	Stars	Language
1	CompOmics/DeepLC DeepLC: Retention time prediction for peptides carrying any modification.	75	Verified	75	Python
2	BojarLab/glycowork Package for processing and analyzing glycans and their role in biology.	64	Established	86	Jupyter Notebook
3	wilhelm-lab/dlomix Python framework for Deep Learning in Proteomics	60	Established	39	Jupyter Notebook
4	BojarLab/CandyCrunch Predicting glycan structure from LC-MS/MS data	59	Established	34	Jupyter Notebook
5	sidhomj/DeepTCR Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data	58	Established	122	Jupyter Notebook
6	MannLabs/alphapeptdeep Deep learning framework for proteomics	55	Established	146	Jupyter Notebook
7	wilhelm-lab/koina Democratizing ML in proteomics	53	Established	52	Jupyter Notebook
8	KrishnaswamyLab/ImmunoStruct [Nature Machine Intelligence] ImmunoStruct enables multimodal deep learning...	51	Established	43	Python
9	wfondrie/depthcharge A deep learning toolkit for mass spectrometry	51	Established	87	Python
10	Noble-Lab/Carafe High quality in silico spectral library generation for data-independent...	47	Emerging	16	Java
11	mnielLab/NetTCR-2.2 Sequence-based prediction of peptide-TCR interactions using paired chain data	47	Emerging	13	Python
12	ProteomicsML/ProteomicsML Community-curated tutorials and datasets for ML in proteomics	46	Emerging	58	Jupyter Notebook
13	jiangdada1221/TCRpeg Deep autoregressive generative models capture the intrinsics embedded in...	45	Emerging	8	Jupyter Notebook
14	caranathunge/promor A comprehensive R package for label-free proteomics data analysis and modeling	43	Emerging	16	R
15	dzjxzyd/UniDL4BioPep webserver	42	Emerging	28	Jupyter Notebook
16	akiyamalab/cycpeptmp Implementation of CycPeptMP, an accurate and efficient model for predicting...	42	Emerging	28	Python
17	EttoreRocchi/ResPredAI Implementation of the pipeline described in the work "Artificial...	42	Emerging	5	Python
18	PaccMann/TITAN Code for "T Cell Receptor Specificity Prediction with Bimodal Attention...	41	Emerging	30	Jupyter Notebook
19	MLCIL/peptides_molecular_fingerprints_classification Code for paper "Molecular Fingerprints Are Strong Models for Peptide...	41	Emerging	4	Jupyter Notebook
20	BojarLab/SweetNet Graph convolutional neural networks for analyzing glycans [LEGACY; use...	38	Emerging	17	Jupyter Notebook
21	Protein-Engineering-Framework/PyPEF PyPEF – Pythonic Protein Engineering Framework	38	Emerging	25	Python
22	Martinaa1408/LB2_project_Group_5 This repository contains the datasets, scripts, and analyses for the...	38	Emerging	3	Jupyter Notebook
23	raghavagps/toxinpred2 An improved method for predicting toxicity of proteins	38	Emerging	18	Perl
24	EMSL-Computing/PeakDecoder A workflow for metabolite identification and accurate profiling in...	37	Emerging	16	R
25	MannLabs/PeptDeep-HLA DL model to predict HLA peptide presentation	37	Emerging	16	Jupyter Notebook
26	EttoreRocchi/MaldiAMRKit Comprehensive toolkit for MALDI-TOF mass spectrometry data preprocessing for...	36	Emerging	2	Jupyter Notebook
27	pengxingang/TEIM TEIM: TCR-Epitope Interaction Modeling	36	Emerging	56	Python
28	BojarLab/LectinOracle Deep learning model to predict interactions between proteins and glycans...	36	Emerging	14	Jupyter Notebook
29	wilhelm-lab/PROSPECT Proteomics Mass Spectrometry Datasets for Machine Learning	36	Emerging	22	Python
30	FennOmix/FennOmix.MHC Foundation model for MHC class I peptide binding prediction built on deep...	35	Emerging	5	Python
31	Wishartlab-openscience/Biotransformer A computational tool for the prediction and identification of metabolites.	34	Emerging	10	Java
32	nec-research/tc-hard Experiments for "On TCR Binding Predictors Failing to Generalize to Unseen...	33	Emerging	8	Jupyter Notebook
33	lkytal/PepNet The state of the art Deep CNN neural network for de novo sequencing of...	33	Emerging	39	Python
34	M-Serajian/MTB-Pipeline MTB++ a software developed to predict antimicrobial resistance to 13...	33	Emerging	3	Python
35	bigict/ProTCR Predicting neoantigen and T-cell receptor binding by integrating structural...	32	Emerging	2	Python
36	HolobiomicsLab/MetaboT 🤖 MetaboT 🍵 is an AI system that accelerates mass spectrometry-based...	32	Emerging	25	Jupyter Notebook
37	molML/peptidy The official codebase of peptidy, a peptide processing tool for machine learning.	31	Emerging	36	Python
38	BioGenies/peptide-prediction-list Collects software dedicated to predicting specific properties of peptides	30	Emerging	68	Shell
39	raghavagps/hemopi2 HemoPI2: Prediction of hemolytic activity of peptides against mammalian RBCs	30	Emerging	13	Python
40	kalininalab/ALPAR Single Reference Antimicrobial Resistance	30	Emerging	7	Python
41	dan-veltri/amp-scanner-v2 Antimicrobial Peptide Scanner Version 2. Open source GLPv3 release of code...	29	Experimental	9	Python
42	kbcoulter/deep_metab Applying Deep Learning Methods to LC-MS Metabolomics Data to Improve...	29	Experimental	6	Python
43	hcji/AutoMS Deep Denoising Autoencoder-assisted Continuous Scoring of Peak Quality in...	29	Experimental	7	Jupyter Notebook
44	XSLiuLab/TLimmuno2 TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning	29	Experimental	12	HTML
45	faezesarlakifar/AllerTrans A Deep Learning Method for Predicting the Allergenicity of Protein Sequences	26	Experimental	6	Jupyter Notebook
46	sablokrep/amnz antimicrobial machine learning	21	Experimental	—	Rust
47	Rishu-raj-02/AMR-Multi-Antibiotic-Resistance-Predictor 🧬 AI-powered multi-task model predicting E. coli resistance to...	21	Experimental	—	HTML
48	Ardit-Mishra/peptide-mhc-binding-predictor A full-stack computational immunology research interface for exploring...	21	Experimental	—	TypeScript
49	JRaviLab/amRml Houses the AMR ML and post-ML package	21	Experimental	—	R
50	PedroSeber/O-GlcNAcylation_Prediction Code and datasets for the publications "Predicting O-GlcNAcylation sites in...	21	Experimental	3	Python
51	AstraBert/resistML A tool for AMR gene family prediction, simple and ML-based	19	Experimental	4	Jupyter Notebook
52	PedroSeber/CHO_N-glycosylation_prediction Code and datasets for the publication "Linear and Neural Network Models for...	18	Experimental	2	Jupyter Notebook
53	musfiquejim/EnACP-A-Hybrid-Machine-Learning-Framework-for-Detecting-Anticancer-Peptides EnACP: একটি Ensemble Learning মডেল যা অ্যান্টিক্যান্সার পেপটাইড সনাক্তকরণের...	17	Experimental	1	Shell
54	NasirNesirli/kleb-amr-project Interpretable Deep-Learning and Ensemble Models for Predicting Multidrug...	14	Experimental	—	HTML
55	AlBadruSsenoga/gritapamr Machine learning (ML) models using sourced data (Antimicrobial Testing...	14	Experimental	—	Jupyter Notebook
56	panos-gbio/Proteomics-in-Latent-Space Repository for my MSc thesis project in Scilifelab - Proteoform Networks...	13	Experimental	—	Jupyter Notebook
57	unumbrela/amp-research2 AMP generation research report with model comparison, evaluation methods,...	13	Experimental	—	TypeScript
58	PulmonomicsLab/mcdr-mtb-standalone Multi-class classification of drug resistance in MTB clinical isolates	11	Experimental	—	Shell
59	vadimnazarov/immunometric Siamese network-based metric learning for dimensionality reduction and visualization	11	Experimental	—	Jupyter Notebook
60	jywangECUST/NR-Profiler We proposed a novel computational framework named NR-Profiler for...	10	Experimental	2	—

Comparisons in this category

DeepTCR and TCRpeg (58 vs 45)