The AI agent for protein bioinformatics. Describe your research goal in plain English — ProteinClaw figures out which tools to call, runs them, and streams a synthesized answer back to you.
Protein research spans dozens of databases — UniProt, BLAST, ClinVar, gnomAD, GTEx, cBioPortal, and more. Moving data between them manually is slow, error-prone, and hard to reproduce.
ProteinClaw replaces that pipeline with a single conversational interface backed by a ReAct agent loop. You describe what you want; the agent decides which tools to call, calls them in sequence, and synthesizes the results into a coherent answer.
- No scripting. Natural language in, structured results out.
- Multi-tool reasoning. The agent chains tools automatically when your question requires it.
- Streaming output. See tool calls, intermediate observations, and the final answer as they happen.
- Your LLM. Works with OpenAI, Anthropic, DeepSeek, MiniMax, or a local Ollama model.
- Your data stays on your machine. ProteinClaw runs entirely on your own computer. Your queries, results, and API keys never pass through any third-party server — nothing is collected, logged, or shared. Use a local Ollama model and no data leaves your machine at all.
A ReAct loop (proteinclaw/core/agent/) that drives all three interfaces:
| Component | What it does |
|---|---|
loop.py |
Thought → Tool Call → Observation cycle, up to 10 steps |
llm.py |
LiteLLM-based multi-model router with async streaming |
prompt.py |
System prompt builder — injects available tools at runtime |
events.py |
Typed event stream: ToolCallEvent, ObservationEvent, TokenEvent, DoneEvent, ErrorEvent |
| Interface | How to launch | Best for |
|---|---|---|
| Terminal UI | proteinclaw |
Interactive multi-turn research sessions |
| One-shot CLI | proteinclaw query "..." |
Scripting, pipelines, quick lookups |
| Desktop App | Tauri .dmg / .exe |
Non-technical users, GUI workflow |
All database integrations live in proteinbox/api_tools/. Each tool is independently testable and auto-discovered by the agent at startup. 53 tools across 15 categories. See Supported Tools for the full list.
A single interactive session walking through all tool categories. The agent automatically chains tools based on each question.
proteinclaw
> What is EGFR and what does it look like structurally?
[tool: uniprot] P00533 — EGFR_HUMAN, receptor tyrosine kinase, 1210 aa, chr 7p11.2
[tool: interpro] 4 domains: Furin-like (×2), Receptor L-domain, Pkinase_Tyr
[tool: panther] PTHR24416:SF85 — Epidermal growth factor receptor; protein class: Receptor kinase
[tool: alphafold] AF-P00533-F1, pLDDT 87.4 (high confidence), full-length model available
[tool: pdb] 7JXR (1.9 Å X-ray, erlotinib-bound), 3NJP (2.8 Å, gefitinib-bound)
[tool: cath] Kinase domain: 3.30.200.20 (Alpha Beta / Sandwich / Protein Kinase)
[tool: scopedb] d.144.1.7 — Protein kinase-like (PK-like) superfamily
[tool: opm] Single-pass type I membrane protein, tilt angle 26°, hydrophobic thickness 30 Å
> How conserved is EGFR and what orthologs exist?
[tool: eggnog] OG: ENOG502S1B9 (Metazoa); COG category: T (Signal transduction); 847 orthologs
[tool: consurf] Kinase domain avg conservation grade: 7.9/9; activation loop (T790) grade: 9 (invariant)
[tool: phylomedb] Phylome 1: 32 orthologs across 28 species; 1:1 orthologs in mouse, zebrafish, Drosophila
> What are the key EGFR variants and their clinical impact?
[tool: clinvar] L858R — Pathogenic (lung adenocarcinoma); T790M — Pathogenic (drug resistance)
[tool: gnomad] pLI 1.00, LOEUF 0.14 — highly constrained; missense z-score 4.5
[tool: uniprot_variants] 287 variants; 14 with clinical significance in kinase domain
[tool: dbsnp] rs121434568 (L858R): AF 0.0001, somatic in lung cancer; rs28929495 (T790M)
[tool: gwas_catalog] 17 GWAS hits: lung cancer risk (p=3×10⁻¹²), breast cancer susceptibility
> What kinase activity data exists for EGFR?
[tool: expasy_enzyme] EC 2.7.10.1 — receptor protein-tyrosine kinase; 312 characterized UniProt entries
[tool: sabio_rk] Km(ATP) = 18 µM (human, pH 7.4, 37°C); kcat = 0.8 s⁻¹ (EGF-activated form)
[tool: brenda] Km(peptide substrate) = 45 µM; optimal pH 7.5; inhibited by erlotinib (IC50 2 nM)
> Where is EGFR expressed at the mRNA and protein level?
[tool: gtex] Highest in skin (42 TPM), kidney cortex (38 TPM), bladder (29 TPM)
[tool: protein_atlas] IHC: strong in liver, kidney, GI tract; subcellular: plasma membrane + endosome
[tool: paxdb] Skin: 524 ppm; kidney: 418 ppm; liver: 187 ppm (integrated proteomics)
[tool: proteomicsdb] Detected in 57/62 tissues; highest MS intensity in epidermis and placenta
> What complexes does EGFR form?
[tool: complex_portal] CPX-906 — EGFR homodimer (EGF-activated); CPX-907 — EGFR:ERBB2 heterodimer
[tool: corum] Complex 5540 — EGFR signalosome: EGFR, GRB2, SOS1, SHC1, GAB1 (HEK293T)
[tool: string] Top partners: ERBB2 (0.999), ERBB3 (0.998), GRB2 (0.994), SRC (0.990)
[tool: intact] 841 curated interactions; top method: anti-bait coimmunoprecipitation
> What drugs target EGFR and what are their binding affinities?
[tool: drugbank] 11 approved drugs; erlotinib — reversible ATP-competitive inhibitor (NSCLC)
[tool: chembl] 147 clinical compounds; 3rd-gen: osimertinib (IC50 1 nM, T790M-selective)
[tool: bindingdb] Erlotinib Kd = 0.4 nM; gefitinib Ki = 0.2 nM; osimertinib IC50 = 1 nM
[tool: dgidb] 34 drug interactions: 28 inhibitors, 3 antibodies (cetuximab, panitumumab)
[tool: opentargets] Top disease: non-small cell lung carcinoma (score 0.95); 11 approved drugs
> What PTMs regulate EGFR and what cancer mutations are known?
[tool: phosphosite] 42 phosphosites; Y1068 (major autophosphorylation); Y1173 (Shc recruitment)
[tool: dbptm] 87 experimentally verified PTMs: 42 phosphorylation, 18 ubiquitination, 6 acetylation
[tool: gene_ontology] BP: transmembrane receptor tyrosine kinase signaling; CC: receptor complex
[tool: cbioportal] EGFR altered in 16% NSCLC (L858R 38%, amplification 22%, T790M 15%)
[tool: disgenet] top disease: lung neoplasms (score 0.9); 47 disease associations total
> What pathways involve EGFR?
[tool: reactome] 51 pathways; top: EGFR Signaling (R-HSA-177929), PI3K/AKT Signaling
[tool: wikipathways] ErbB signaling (WP673), MAPK cascade (WP382), Focal Adhesion (WP306)
[tool: kegg] hsa04012 (ErbB signaling), hsa05223 (non-small cell lung cancer)
> Find recent papers on EGFR resistance mechanisms
[tool: literature] Searched PubMed, Europe PMC, Semantic Scholar, CrossRef, bioRxiv, arXiv
Top result: "Osimertinib resistance: mechanisms and clinical implications"
Nature Reviews Cancer 2024 — 312 citations
[tool: pubmed] 847 articles for "EGFR resistance"; 43 reviews in last 2 years
Immune gene quick lookup (uses imgt):
proteinclaw
> Characterize the IGHV1-2 germline gene
[tool: imgt] IGHV1-2*02 — functional allele, chromosome 14q32.33
CDR1 length 8 aa, CDR2 length 8 aa; 99.6% identity to IGHV1-2*01
Used in 12% of mature B-cell repertoires; associated with anti-VRC01 broadly neutralizing antibodies
One-shot mode:
proteinclaw query "What clinical variants are reported for BRCA1?"
proteinclaw query --model gpt-4o "Summarize the GTEx expression profile of TP53"
proteinclaw query "Is rs1801133 a pathogenic variant?"
proteinclaw query "What kinetic parameters are known for EC 2.7.10.1?"
proteinclaw query "What drugs bind EGFR and what are their affinities?"Example queries by category:
| Category | Query | Tools invoked |
|---|---|---|
| Annotation | What is P04637? |
uniprot → interpro → panther |
| Structure | Show me EGFR structures and classify its domains |
pdb → alphafold → cath → scopedb |
| Membrane | Is EGFR a membrane protein? What's its orientation? |
opm |
| Evolution | How conserved is the EGFR kinase domain across species? |
eggnog → consurf → phylomedb |
| Sequence | Find proteins similar to this sequence: <FASTA> |
blast → elm → disprot → mobidb |
| Variants | What variants are reported for BRCA1? |
clinvar → gnomad → uniprot_variants |
| Kinetics | What are the kinetic parameters of EC 2.7.10.1? |
expasy_enzyme → sabio_rk → brenda |
| Expression | Where is TP53 expressed at mRNA and protein level? |
gtex → protein_atlas → paxdb → proteomicsdb |
| Complexes | What protein complexes does EGFR form? |
complex_portal → corum |
| Interactions | Who are EGFR's top interaction partners? |
string → intact |
| Drug & Binding | What drugs target EGFR and how tightly do they bind? |
drugbank → chembl → bindingdb → dgidb |
| Disease | What diseases are linked to TP53? |
opentargets → disgenet → omim |
| PTM | What post-translational modifications regulate EGFR? |
phosphosite → dbptm |
| Cancer | Tell me about TP53 mutations in lung cancer |
cbioportal → uniprot_variants |
| Pathways | What pathways does EGFR participate in? |
reactome → wikipathways → kegg |
| Immunology | Characterize the IGHV1-2 germline gene |
imgt |
| Proteomics | Find public proteomics datasets for EGFR |
pride |
| Literature | Recent papers on EGFR resistance |
literature → pubmed |
TUI slash commands:
| Command | Effect |
|---|---|
/model <name> |
Switch LLM model for this session |
/tools |
List all registered tools |
/clear |
Clear conversation history |
/quit |
Exit |
macOS / Linux:
curl -fsSL https://raw.githubusercontent.com/shuaizengMU/ProteinClaw/main/install.sh | bashWindows (PowerShell):
irm https://raw.githubusercontent.com/shuaizengMU/ProteinClaw/main/install.ps1 | iexThe script will:
- Install uv if not already present
- Install the ProteinClaw Python backend via
uv tool install - Download the
proteinclaw-tuibinary for your platform from the latest release - Add
~/.local/binto yourPATHif needed
On first launch, a setup wizard prompts for your API key and default model. Settings are saved to ~/.config/proteinclaw/config.toml.
git clone https://github.com/shuaizengMU/ProteinClaw.git
cd ProteinClaw
uv sync
bash scripts/build-tui.sh
cp target/release/proteinclaw-tui ~/.local/bin/
proteinclaw-tuiYou only need one key to get started.
| Variable | Provider | Required |
|---|---|---|
OPENAI_API_KEY |
OpenAI | If using GPT-4o |
ANTHROPIC_API_KEY |
Anthropic | If using Claude |
DEEPSEEK_API_KEY |
DeepSeek | If using DeepSeek |
MINIMAX_API_KEY |
MiniMax | If using MiniMax |
NCBI_API_KEY |
NCBI | Optional — raises BLAST rate limit |
DRUGBANK_TOKEN |
DrugBank | Optional — enables drugbank tool (free registration at drugbank.com) |
BRENDA_EMAIL + BRENDA_PASSWORD |
BRENDA | Optional — enables brenda tool (free registration at brenda-enzymes.org) |
53 tools across 15 categories. API = calls an external database. Local = runs entirely on-device, no network required. Tools marked † require free registration (see API Keys).
| Category | Tool | Type | Database / Source | What it fetches |
|---|---|---|---|---|
| Protein Annotation | uniprot |
API | UniProt | Name, function, genes, organism, sequence length, GO terms |
interpro |
API | InterPro (EBI) | Domain/family annotations from Pfam, PROSITE, CDD with coordinates | |
panther |
API | PANTHER | Family/subfamily classification, protein class, GO slim | |
gene_ontology |
API | QuickGO (EBI) | GO annotations by molecular function, biological process, cellular component | |
phosphosite |
API | UniProt PTM | Post-translational modifications (phosphorylation, ubiquitination, acetylation) with positions | |
expasy_protparam |
Local | — | MW, pI, GRAVY, instability index, signal peptide and TM helix prediction | |
sequence_analysis |
Local | — | MW, isoelectric point, GRAVY, amino acid composition, extinction coefficients | |
| Protein Structure | alphafold |
API | AlphaFold DB (EBI) | Predicted structure, pLDDT confidence score, sequence coverage, model version |
pdb |
API | RCSB Protein Data Bank | Structure metadata: method, resolution, organism, deposit date, chains, ligands | |
cath |
API | CATH Structural DB | Domain classification: Class, Architecture, Topology, Homology hierarchy | |
scopedb |
API | SCOPe | SCOP class, fold, superfamily, and family for each PDB domain | |
opm |
API | OPM (MPSTRUC) | Membrane protein orientation: tilt angle, hydrophobic thickness, topology type | |
| Sequence & Motifs | blast |
API | NCBI BLAST | Sequence similarity against NR database; E-values, percent identity |
elm |
Local | — | Short linear motif predictions: binding sites, modification sites, degradation signals | |
disprot |
API | DisProt | Experimentally validated intrinsically disordered regions with coordinates and evidence | |
mobidb |
API | MobiDB | Disorder consensus regions, curated disorder annotations | |
| Protein Evolution | eggnog |
API | eggNOG v6 | Orthologous group ID, COG functional category, GO terms, species coverage |
consurf |
API | ConSurf DB | Per-residue conservation grades (1–9), functional residue flags | |
phylomedb |
API | PhylomeDB | Phylome IDs, 1:1/1:N orthologs with species and identity scores, paralogs | |
| Variants & Clinical | clinvar |
API | ClinVar (NCBI) | Clinical significance by gene; pathogenic/benign calls, associated conditions |
dbsnp |
API | dbSNP (NCBI) | SNP details by rsID: position, alleles, clinical significance, minor allele frequency | |
gnomad |
API | gnomAD (Broad) | Gene constraint metrics: pLI, LOEUF, missense constraint | |
uniprot_variants |
API | EBI Proteins API | Known protein variants with clinical significance, consequence type, position | |
gwas_catalog |
API | GWAS Catalog (EBI) | GWAS associations by gene: traits, SNP rsIDs, p-values, risk alleles | |
| Gene & Genomics | ensembl |
API | Ensembl REST API | Gene/transcript IDs, genomic coordinates, biotype, orthologs, cross-references |
ncbi_gene |
API | NCBI Gene (Entrez) | Gene ID, aliases, organism, chromosome location, summary | |
kegg |
API | KEGG REST API | KEGG pathway IDs and names for a gene | |
| Enzyme / Metabolism | expasy_enzyme |
API | ExPASy ENZYME | EC number, accepted name, reaction equation, cofactors, UniProt entry count |
sabio_rk |
API | SABIO-RK | Km, kcat, Vmax with organism, pH, temperature, and PubMed reference | |
brenda † |
API | BRENDA | Km values, substrates, inhibitors, cofactors, optimal pH/temperature | |
| Pathways & Interactions | reactome |
API | Reactome | Biological pathways with names, species, diagram availability, sub-pathways |
wikipathways |
API | WikiPathways | Pathways by gene/term: IDs, names, species, revision dates | |
string |
API | STRING Database | Protein-protein interactions: top partners with combined and interaction scores | |
intact |
API | IntAct (EBI) | Curated binary protein interactions with detection methods, MI scores | |
| Protein Complexes | complex_portal |
API | Complex Portal (EBI) | Experimentally validated complexes: subunits, stoichiometry, GO terms |
corum |
API | CORUM | Curated mammalian complexes: subunit list, purification method, tissue, disease | |
| Disease & Drug | opentargets |
API | Open Targets Platform | Target-disease associations with evidence scores, known drugs, tractability |
chembl |
API | ChEMBL (EBI) | Drug-target interactions: approved drugs and clinical candidates with mechanisms | |
disgenet |
API | DisGeNET + NCBI | Disease-gene associations with scores; NCBI fallback for Mendelian disease entries | |
omim |
API | OMIM (via NCBI) | Genetic disease associations via NCBI Gene → OMIM linkage | |
cbioportal |
API | cBioPortal | Cancer genomics: gene type, cytoband, mutation landscape across 535+ cancer studies | |
| Drug & Binding Affinity | drugbank † |
API | DrugBank | Mechanism of action, pharmacodynamics, ADMET, indications, targets |
bindingdb |
API | BindingDB | Protein-ligand Ki, Kd, IC50 values with assay type and organism | |
dgidb |
API | DGIdb | Drug-gene interactions: drug names, interaction types (inhibitor/activator/antibody) | |
| PTM & Structural | dbptm |
API | dbPTM | Experimentally verified PTMs: type, residue position, kinase (if phosphorylation) |
imgt |
API | IMGT | Immunoglobulin, TCR, and MHC gene classification, alleles, chromosomal location | |
| Expression | gtex |
API | GTEx Portal | Tissue-specific gene expression (median TPM) across human tissues |
protein_atlas |
API | Human Protein Atlas | Tissue expression, IHC detection, subcellular localization, cancer specificity | |
| Proteomics / Abundance | paxdb |
API | PaxDb | Protein abundance in ppm across tissues and species (integrated proteomics) |
proteomicsdb |
API | ProteomicsDB | MS intensity by tissue and cell line, peptide detectability | |
pride |
API | PRIDE Archive | Public proteomics dataset accessions, species, submission dates, PubMed links | |
| Literature | pubmed |
API | PubMed (NCBI eUtils) | Article titles, authors, journal, year, abstract snippets |
literature |
API | PubMed · Europe PMC · Semantic Scholar · CrossRef · bioRxiv · arXiv | Searches 6 sources in parallel, deduplicates by DOI, merges results with citation counts |
MIT