Protein Property Prediction Embedding Tools

Tools for predicting biological properties, functions, and characteristics of proteins, peptides, RNA, and related biomolecules using language models and machine learning. Does NOT include general protein structure prediction, sequence alignment, or embeddings-only libraries without downstream prediction tasks.

There are 22 protein property prediction tools tracked. The highest-rated is DeepChainBio/bio-transformers at 39/100 with 155 stars.

Get all 22 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=embeddings&subcategory=protein-property-prediction&limit=20"

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#	Tool	Score	Tier	Stars	Language
1	DeepChainBio/bio-transformers bio-transformers is a wrapper on top of the ESM/Protbert model, trained on...	39	Emerging	155	Python
2	Rostlab/bindPredict Prediction of binding residues for metal ions, nucleic acids, and small molecules.	35	Emerging	35	Python
3	bio-ontology-research-group/predCAN Ontology-based prediction of cancer driver genes	28	Experimental	5	Python
4	MI2DataLab/memr R package for Multisource Embeddings for Medical Records	28	Experimental	17	R
5	KCLabMTU/LMSuccSite Improving Protein Succinylation Sites Prediction Using Features Extracted...	26	Experimental	1	Jupyter Notebook
6	thrakar9/CoMET Learning hierarchical motif representations for proteins.	26	Experimental	6	Python
7	adenger/subpred_dl Code for the manuscript "Application of Protein Structure Encodings and...	24	Experimental	1	Jupyter Notebook
8	CBBIO/protein-information-system Functional sequence annotation, metamorphism and multifunctionality research...	24	Experimental	7	Python
9	nanxstats/exp2vec 🧬 Tissue-specific gene embeddings trained on GTEx data	23	Experimental	2	R
10	ixcor/omics-survival-embeddings 🌱 Benchmark embedding methods for survival prediction on omics data,...	22	Experimental	—	Jupyter Notebook
11	carlomazzaferro/mhcPreds MHC-antigen affinity prediction using TensorFlow.	18	Experimental	7	Jupyter Notebook
12	KonNik88/omics-survival-embeddings Benchmarking embedding methods (UMAP, VAE, PCA, FA, ICA, etc.) for survival...	18	Experimental	4	Jupyter Notebook
13	sinc-lab/Comparison-of-Protein-learning Comparison of protein learning	17	Experimental	4	Jupyter Notebook
14	wmmthu/REGENT Integrating embeddings of multiple gene networks to prioritize complex...	16	Experimental	3	R
15	HsiaoYetGun/MiRLocator miRNA subcellular localization	15	Experimental	2	Python
16	damianosmel/dom2vec dom2vec: Protein domain embeddings	13	Experimental	7	Python
17	suraj5424/Protein-sequence-analysis This notebook does the analysis of a protein sequence dataset in FASTA...	12	Experimental	3	Jupyter Notebook
18	akash18tripathi/MAGNET-Multi-Label-Text-Classi-cation-using-Attention-based-Graph-Neural-Network This GitHub repository provides an implementation of the paper "MAGNET:...	12	Experimental	20	Jupyter Notebook
19	DarkAdin/ESM2_15B ESM2-15B Protein Embeddings	11	Experimental	—	Jupyter Notebook
20	lueasf/toxipep Peptide Toxicity Prediction with pLM Embeddings.	11	Experimental	—	Jupyter Notebook
21	hallamlab/reMap reMap: relabeling metabolic pathway data with groups to improve prediction outcomes	10	Experimental	1	Python
22	biocentral/bio_ml_models Collection of prediction models for biological tasks	10	Experimental	1	Python