Protein Design LLMs LLM Tools

LLM and language model tools specifically for protein engineering, design, and prediction tasks. Includes protein sequence analysis, directed evolution, antibody design, and protein property prediction. Does NOT include general drug discovery, small molecule design, or non-protein biological sequence tools.

There are 33 protein design llms tools tracked. 5 score above 50 (established tier). The highest-rated is cafferychen777/mLLMCelltype at 62/100 with 635 stars. 1 of the top 10 are actively maintained.

Get all 33 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=llm-tools&subcategory=protein-design-llms&limit=20"

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#	Tool	Score	Tier	Stars	Language
1	cafferychen777/mLLMCelltype Cell type annotation for single-cell RNA-seq using multi-LLM consensus	62	Established	635	R
2	NygenAnalytics/CyteType Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data	60	Established	117	Python
3	alibaba/LucaProt LucaProt: A novel deep learning framework that incorporates protein amino...	56	Established	223	Python
4	LucaOne/LucaOne The resources of LucaOne, including: the model code, training scripts,...	52	Established	357	Python
5	monarch-initiative/curategpt LLM-driven curation assist tool	50	Established	102	Jupyter Notebook
6	LucaOne/LucaPCycle We developed a dual-channel model named LucaPCycle, based on the raw...	49	Emerging	34	Python
7	silicobio/peleke 🦋 peleke-1: Protein Language Models for Targeted Antibody Design	43	Emerging	7	C
8	prototypo/ethereum-eips-ontology An ontology of Ethereum terms extracted from the Ethereum glossaries and...	42	Emerging	44	Python
9	LucaOne/LucaVirus LucaVirus: Modeling the Evolutionary and Functional Landscape of Viruses...	39	Emerging	63	Python
10	OviaLabs/ProteinGPT ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure...	39	Emerging	33	Python
11	bunyaminergen/Callytics Callytics is an advanced call analytics solution that leverages speech...	38	Emerging	78	Python
12	chao1224/ProteinDT A Text-guided Protein Design Framework, Nat Mach Intell 2025...	36	Emerging	102	Python
13	DaoyuanLi2816/Kaggle-4th-Place-Solution-LMSYS-Chatbot-Arena-Human-Preference-Predictions 4th Place Solution for the Kaggle Competition: LMSYS - Chatbot Arena Human...	36	Emerging	170	Jupyter Notebook
14	NygenAnalytics/CyteTypeR Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data	32	Emerging	31	R
15	Ohyeon5/syn-search Optimal Drug Synthesis Condition Searching Conversational AI, using LLMs	32	Emerging	3	Python
16	blazerye/DrugAssist [Briefings In Bioinformatics] DrugAssist: A Large Language Model for...	31	Emerging	140	Python
17	GeneralSubhra/variant-analysis-evo2 a web app that can classify how likely specific mutations in DNA are to...	29	Experimental	16	TypeScript
18	monarch-initiative/phenomics-assistant LLM retrieval augmented generation agent for the Monarch Knowledge graph.	29	Experimental	27	Python
19	chao1224/ChatDrug LLM for Drug Editing, ICLR 2024	28	Experimental	157	Python
20	raghavagps/antifp2 Prediction of anti-fungal proteins using protein language models	28	Experimental	3	Python
21	DavidAI2024/DrugGeneExplorer This Python script is designed to provide detailed information on...	28	Experimental	5	Python
22	westlake-repl/ProteinLM-TDG2-Mutation Protein language models-assisted optimization of a uracil-N-glycosylase...	27	Experimental	18	Jupyter Notebook
23	JanaShenLab/AiPP_v1 Artificial Intelligence Protein Profiling	23	Experimental	1	Python
24	ianmkim/genomicGPT An experiment annotating protein sequences using pretrained LLMs GPT-3 and OPT-2.7B	20	Experimental	5	Python
25	monarch-initiative/dppkb DEMO example knowledge base created using DRAGON-AI	20	Experimental	5	HTML
26	LokaHQ/Trinity-Mini-DrugProt-Think Trinity-Mini-DrugProt-Think	18	Experimental	9	HTML
27	junayed-hasan/Life-Satisfaction-Machine-Learning This repo contains code for predicting life satisfaction using machine...	18	Experimental	2	Jupyter Notebook
28	awsaf49/lmsys LMSYS - Chatbot Arena Human Preference Predictions \| Predicting Human...	18	Experimental	2	Jupyter Notebook
29	niphoenixo/kaggle-llm-competition Kaggle LLM Classification Competition - Predicting human preferences between...	18	Experimental	2	Python
30	EhsanBitaraf/ai-powered-affiliation-extraction 📝✍️AI-Powered Affiliation Insights: LLM-Based Bibliometric Study of European...	15	Experimental	—	Jupyter Notebook
31	Vcarmelli/Internship-AI-drug-discovery A web application focuses on visualizing molecular docking results for...	13	Experimental	—	HTML
32	skerk001/genomicsgpt ML + LLM pipeline for genetic variant pathogenicity prediction (AUC 0.9949,...	13	Experimental	—	Jupyter Notebook
33	Nauman123-coder/GNN-LLM-Mutagen-Agent A hybrid AI system for molecular safety screening. Combines a Graph...	12	Experimental	1	Jupyter Notebook

Comparisons in this category

mLLMCelltype and CyteType (62 vs 60) mLLMCelltype and CyteTypeR (62 vs 32)