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 46 protein design llms tools tracked. 2 score above 50 (established tier). The highest-rated is NygenAnalytics/CyteType at 64/100 with 117 stars and 1,232 monthly downloads. 1 of the top 10 are actively maintained.

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#	Tool	Score	Tier	Stars	Language
1	NygenAnalytics/CyteType Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data	64	Established	117	Python
2	cafferychen777/mLLMCelltype Cell type annotation for single-cell RNA-seq using multi-LLM consensus	55	Established	635	R
3	alibaba/LucaProt LucaProt: A novel deep learning framework that incorporates protein amino...	49	Emerging	223	Python
4	LucaOne/LucaOne The resources of LucaOne, including: the model code, training scripts,...	45	Emerging	357	Python
5	monarch-initiative/curategpt LLM-driven curation assist tool	43	Emerging	102	Jupyter Notebook
6	LucaOne/LucaPCycle We developed a dual-channel model named LucaPCycle, based on the raw...	42	Emerging	34	Python
7	silicobio/peleke 🦋 peleke-1: Protein Language Models for Targeted Antibody Design	37	Emerging	7	C
8	prototypo/ethereum-eips-ontology An ontology of Ethereum terms extracted from the Ethereum glossaries and...	35	Emerging	44	Python
9	OviaLabs/ProteinGPT ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure...	34	Emerging	33	Python
10	LucaOne/LucaVirus LucaVirus: Modeling the Evolutionary and Functional Landscape of Viruses...	33	Emerging	63	Python
11	bunyaminergen/Callytics Callytics is an advanced call analytics solution that leverages speech...	33	Emerging	78	Python
12	tirtharajdash/LMLFStar Generating target-specific novel lead molecules using an LLM	30	Emerging	4	HTML
13	DaoyuanLi2816/Kaggle-4th-Place-Solution-LMSYS-Chatbot-Arena-Human-Preference-Predictions 4th Place Solution for the Kaggle Competition: LMSYS - Chatbot Arena Human...	29	Experimental	170	Jupyter Notebook
14	chao1224/ProteinDT A Text-guided Protein Design Framework, Nat Mach Intell 2025...	29	Experimental	102	Python
15	NygenAnalytics/CyteTypeR Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data	29	Experimental	31	R
16	raghavagps/pptstab PPTStab: Designing of thermostable proteins with a desired melting temperature	28	Experimental	6	Python
17	DavidAI2024/DrugGeneExplorer This Python script is designed to provide detailed information on...	26	Experimental	5	Python
18	GeneralSubhra/variant-analysis-evo2 a web app that can classify how likely specific mutations in DNA are to...	25	Experimental	16	TypeScript
19	Ohyeon5/syn-search Optimal Drug Synthesis Condition Searching Conversational AI, using LLMs	25	Experimental	3	Python
20	blazerye/DrugAssist [Briefings In Bioinformatics] DrugAssist: A Large Language Model for...	24	Experimental	140	Python
21	raghavagps/NTxPred2 NTxPred2: An improved method for predicting neurotoxicity of peptides and proteins	23	Experimental	3	Python
22	monarch-initiative/phenomics-assistant LLM retrieval augmented generation agent for the Monarch Knowledge graph.	22	Experimental	27	Python
23	kenflab/LLM-scCurator Data-centric marker distillation for zero-shot cell-type and spatial...	22	Experimental	3	Jupyter Notebook
24	raghavagps/antifp2 Prediction of anti-fungal proteins using protein language models	22	Experimental	3	Python
25	chao1224/ChatDrug LLM for Drug Editing, ICLR 2024	21	Experimental	157	Python
26	westlake-repl/ProteinLM-TDG2-Mutation Protein language models-assisted optimization of a uracil-N-glycosylase...	20	Experimental	18	Jupyter Notebook
27	raghavagps/cytolncpred CytoLNCpred: A method for predicting cytoplasm associate lncRNA	20	Experimental	2	Python
28	raghavagps/IonNTxPred Large language models for predicting ion channels modulating proteins	19	Experimental	—	Python
29	LiLabTsinghua/D2Cell Learn to predict in metabolic engineering	19	Experimental	—	Python
30	Shreyas-Bhat/LMLF Code for "Generating Novel Leads for Drug Discovery Using LLMs with Logical...	18	Experimental	7	Python
31	raghavagps/il2pred Prediction of IL2 inducing peptides	18	Experimental	3	Python
32	niphoenixo/kaggle-llm-competition Kaggle LLM Classification Competition - Predicting human preferences between...	16	Experimental	2	Python
33	JanaShenLab/AiPP_v1 Artificial Intelligence Protein Profiling	16	Experimental	1	Python
34	LokaHQ/Trinity-Mini-DrugProt-Think Trinity-Mini-DrugProt-Think	16	Experimental	9	HTML
35	Haozhou98/hdd-SMART-fd-with-dt-llm-hpo HDD failure prediction from SMART logs using a Decision Tree;...	15	Experimental	—	Jupyter Notebook
36	skerk001/genomicsgpt ML + LLM pipeline for genetic variant pathogenicity prediction (AUC 0.9949,...	14	Experimental	—	Jupyter Notebook
37	monarch-initiative/dppkb DEMO example knowledge base created using DRAGON-AI	13	Experimental	5	HTML
38	EhsanBitaraf/ai-powered-affiliation-extraction 📝✍️AI-Powered Affiliation Insights: LLM-Based Bibliometric Study of European...	13	Experimental	—	Jupyter Notebook
39	ianmkim/genomicGPT An experiment annotating protein sequences using pretrained LLMs GPT-3 and OPT-2.7B	13	Experimental	5	Python
40	Zack4DEV/cellpose_sam_spheres Cell seeding efficiency measurement using customized Cellpose SAM...	12	Experimental	1	Jupyter Notebook
41	Tamanna-Sharma8/llm-classification-finetuning-kaggle Kaggle LLM Classification Competition - Predicting human preferences between...	11	Experimental	—	Jupyter Notebook
42	maris205/biopaws Emergence of Biological Structural Discovery in General-Purpose Language Models	11	Experimental	—	Jupyter Notebook
43	junayed-hasan/Life-Satisfaction-Machine-Learning This repo contains code for predicting life satisfaction using machine...	11	Experimental	2	Jupyter Notebook
44	awsaf49/lmsys LMSYS - Chatbot Arena Human Preference Predictions \| Predicting Human...	11	Experimental	2	Jupyter Notebook
45	Vcarmelli/Internship-AI-drug-discovery A web application focuses on visualizing molecular docking results for...	11	Experimental	—	HTML
46	HassanMahmoodKhan/Strawberry-Variety-Identification Employs a CNN-based multi-class strawberry variety classification. The...	11	Experimental	2	Python

Comparisons in this category

CyteType and mLLMCelltype (64 vs 55) mLLMCelltype and CyteTypeR (55 vs 29)