Labmate Mcp
Connects Claude to 25+ scientific APIs covering the full chemistry research workflow. Out of the box you get PubChem compound lookups, Crossref and Semantic Scholar literature search, RCSB protein structures, MassBank spectra, and BindingDB affinity data. Optional free API keys unlock IBM RXN retrosynthesis, Rowan Science pKa prediction, and NMRShiftDB chemical shift lookups. Also includes 30 bench reference tools like reagent calculators, protecting group selectors, named reaction templates for 202 transformations, solvent tables, and cooling bath guides. Publication helpers generate BibTeX citations and format experimental procedures. Reach for this when you need Claude to search papers, plan syntheses, calculate stoichiometry, look up safety data, or draft experimental sections without switching between a dozen chemistry websites.
- GitHub stars
- 1
- tools
- 80
- auth
- Secret needed
- transport
- STDIO
- env vars
- 2
- last updated
- Feb 2, 2026
Tools
80 toolsPublic tool metadata for what this MCP can expose to an agent.
search_papersMulti-source paper search with metadata fusion.
Multi-source paper search with metadata fusion.
No parameter schema in public metadata yet.
get_paper_detailsFull metadata: abstract, authors, citations, references.
Full metadata: abstract, authors, citations, references.
No parameter schema in public metadata yet.
find_similar_papersContent-based paper recommendations.
Content-based paper recommendations.
No parameter schema in public metadata yet.
get_paper_citationsForward citation graph + context snippets.
Forward citation graph + context snippets.
No parameter schema in public metadata yet.
get_paper_referencesBackward citation graph (bibliography).
Backward citation graph (bibliography).
No parameter schema in public metadata yet.
get_author_profileh-index, publications, co-authors, topics.
h-index, publications, co-authors, topics.
No parameter schema in public metadata yet.
analyze_research_topicPublication volume trends over time.
Publication volume trends over time.
No parameter schema in public metadata yet.
find_open_access_pdfLegal open access PDF URLs.
Legal open access PDF URLs.
No parameter schema in public metadata yet.
search_chemrxivChemistry preprint search.
Chemistry preprint search.
No parameter schema in public metadata yet.
get_chemrxiv_categoriesList ChemRxiv subject categories.
List ChemRxiv subject categories.
No parameter schema in public metadata yet.
search_web_of_scienceWoS search (requires API key).
WoS search (requires API key).
No parameter schema in public metadata yet.
generate_bibtexDOI to BibTeX (single or batch).
DOI to BibTeX (single or batch).
No parameter schema in public metadata yet.
get_journal_metricsImpact metrics, open access %, policy.
Impact metrics, open access %, policy.
No parameter schema in public metadata yet.
search_protein_structuresSearch PDB by keyword, organism, method.
Search PDB by keyword, organism, method.
No parameter schema in public metadata yet.
get_protein_structureFull PDB entry: resolution, ligands, sequence.
Full PDB entry: resolution, ligands, sequence.
No parameter schema in public metadata yet.
search_compoundName/SMILES/formula to compound data.
Name/SMILES/formula to compound data.
No parameter schema in public metadata yet.
get_compound_propertiesMW, SMILES, InChI, formula, XLogP, TPSA.
MW, SMILES, InChI, formula, XLogP, TPSA.
No parameter schema in public metadata yet.
profile_compoundComprehensive profile combining several databases.
Comprehensive profile combining several databases.
No parameter schema in public metadata yet.
get_safety_dataGHS pictograms, H-statements, P-statements.
GHS pictograms, H-statements, P-statements.
No parameter schema in public metadata yet.
translate_compound_idsConvert PubChem, ChEMBL, DrugBank, ChEBI IDs.
Convert PubChem, ChEMBL, DrugBank, ChEBI IDs.
No parameter schema in public metadata yet.
search_crystal_structuresCrystallography Open Database search.
Crystallography Open Database search.
No parameter schema in public metadata yet.
search_materials_projectBand gaps, formation energies (requires key).
Band gaps, formation energies (requires key).
No parameter schema in public metadata yet.
search_nist_webbookΔHf, Cp, phase transitions, IR spectra.
ΔHf, Cp, phase transitions, IR spectra.
No parameter schema in public metadata yet.
search_mass_spectraMass spectrum search by exact mass or name.
Mass spectrum search by exact mass or name.
No parameter schema in public metadata yet.
search_binding_dataIC50, Ki, Kd binding affinities.
IC50, Ki, Kd binding affinities.
No parameter schema in public metadata yet.
search_toxicityToxicity endpoints (requires key).
Toxicity endpoints (requires key).
No parameter schema in public metadata yet.
classify_natural_productNP superclass / class / pathway.
NP superclass / class / pathway.
No parameter schema in public metadata yet.
predict_retrosynthesisMulti-step retrosynthetic analysis.
Multi-step retrosynthetic analysis.
No parameter schema in public metadata yet.
plan_synthesisForward synthesis route planning.
Forward synthesis route planning.
No parameter schema in public metadata yet.
predict_productPredict products from reactants + reagents.
Predict products from reactants + reagents.
No parameter schema in public metadata yet.
predict_atom_mappingAtom-by-atom mapping for mechanisms.
Atom-by-atom mapping for mechanisms.
No parameter schema in public metadata yet.
text_to_procedureNatural language to structured procedure.
Natural language to structured procedure.
No parameter schema in public metadata yet.
predict_pkapKa values (any functional group, aqueous).
pKa values (any functional group, aqueous).
No parameter schema in public metadata yet.
predict_solubilityAqueous solubility prediction.
Aqueous solubility prediction.
No parameter schema in public metadata yet.
predict_admetAbsorption, metabolism, toxicity prediction.
Absorption, metabolism, toxicity prediction.
No parameter schema in public metadata yet.
search_tautomersEnumerate tautomeric forms.
Enumerate tautomeric forms.
No parameter schema in public metadata yet.
compute_descriptorsMolecular descriptors from SMILES.
Molecular descriptors from SMILES.
No parameter schema in public metadata yet.
predict_nmr1H and 13C chemical shift prediction.
1H and 13C chemical shift prediction.
No parameter schema in public metadata yet.
peptide_to_smilesSequence to SMILES (450+ AAs, 5 cyclization types).
Sequence to SMILES (450+ AAs, 5 cyclization types).
No parameter schema in public metadata yet.
peptide_cyclization_optionsWhich cyclizations does a sequence support?
Which cyclizations does a sequence support?
No parameter schema in public metadata yet.
generate_peptide_libraryRandom peptide generation with NCAAs, D-stereo.
Random peptide generation with NCAAs, D-stereo.
No parameter schema in public metadata yet.
peptide_propertiesMW, logP, TPSA, HBD/HBA, Lipinski.
MW, logP, TPSA, HBD/HBA, Lipinski.
No parameter schema in public metadata yet.
check_peptide_synthesisSPPS feasibility: difficult motifs, aggregation.
SPPS feasibility: difficult motifs, aggregation.
No parameter schema in public metadata yet.
modify_peptideApply N-methylation, PEGylation.
Apply N-methylation, PEGylation.
No parameter schema in public metadata yet.
calculate_peptide_piIsoelectric point (8 pKa reference sets).
Isoelectric point (8 pKa reference sets).
No parameter schema in public metadata yet.
calculate_peptide_extinctionε280 (Trp/Tyr/Cys contributions).
ε280 (Trp/Tyr/Cys contributions).
No parameter schema in public metadata yet.
get_peptide_ion_seriesb/y/a/c/z ion ladders for MS/MS.
b/y/a/c/z ion ladders for MS/MS.
No parameter schema in public metadata yet.
assign_peptide_ms_peaksMatch m/z values to fragments.
Match m/z values to fragments.
No parameter schema in public metadata yet.
calculate_molaritySolve for any unknown: mass, moles, volume, or MW.
Solve for any unknown: mass, moles, volume, or MW.
No parameter schema in public metadata yet.
calculate_dilutionC1V1 = C2V2 with automatic unit handling.
C1V1 = C2V2 with automatic unit handling.
No parameter schema in public metadata yet.
calculate_reaction_massMulti-reagent mass calc from equivalents.
Multi-reagent mass calc from equivalents.
No parameter schema in public metadata yet.
calculate_yieldPercent yield from actual / theoretical.
Percent yield from actual / theoretical.
No parameter schema in public metadata yet.
calculate_concentrationM, mM, mg/mL, %w/v, ppm, ppb conversions.
M, mM, mg/mL, %w/v, ppm, ppb conversions.
No parameter schema in public metadata yet.
lookup_named_reaction202 named reactions: conditions, mechanism, scope, limitations.
202 named reactions: conditions, mechanism, scope, limitations.
No parameter schema in public metadata yet.
lookup_rxn_dev_checklistStructured checklist for reaction development.
Structured checklist for reaction development.
No parameter schema in public metadata yet.
lookup_protecting_group30 PGs for OH, NH, C=O, COOH with stability matrix.
30 PGs for OH, NH, C=O, COOH with stability matrix.
No parameter schema in public metadata yet.
lookup_workup_procedureStep-by-step protocols: LAH quench, aqueous extraction, etc.
Step-by-step protocols: LAH quench, aqueous extraction, etc.
No parameter schema in public metadata yet.
lookup_solvent_properties32 solvents: bp, density, polarity, dielectric, miscibility.
32 solvents: bp, density, polarity, dielectric, miscibility.
No parameter schema in public metadata yet.
lookup_cooling_bath24 recipes from -196 °C to +100 °C.
24 recipes from -196 °C to +100 °C.
No parameter schema in public metadata yet.
lookup_tlc_stain13 stains organized by functional group selectivity.
13 stains organized by functional group selectivity.
No parameter schema in public metadata yet.
lookup_column_chromatographySolvent selection, Rf rules, loading, troubleshooting.
Solvent selection, Rf rules, loading, troubleshooting.
No parameter schema in public metadata yet.
lookup_buffer_recipe20+ buffers: PBS, Tris, HEPES, TAE, TBE, RIPA, citrate.
20+ buffers: PBS, Tris, HEPES, TAE, TBE, RIPA, citrate.
No parameter schema in public metadata yet.
lookup_amino_acid_properties20 canonical AAs: MW, pKa, pI, hydropathy.
20 canonical AAs: MW, pKa, pI, hydropathy.
No parameter schema in public metadata yet.
lookup_nmr_solvent12 solvents: residual 1H/13C shifts, water peak, multiplicity.
12 solvents: residual 1H/13C shifts, water peak, multiplicity.
No parameter schema in public metadata yet.
lookup_lab_tips35 practical tips across 9 categories.
35 practical tips across 9 categories.
No parameter schema in public metadata yet.
lookup_safety_card9 safety cards for hazardous reagents.
9 safety cards for hazardous reagents.
No parameter schema in public metadata yet.
calculate_isotope_patternIsotope distribution from formula/SMILES (Cl, Br, S patterns).
Isotope distribution from formula/SMILES (Cl, Br, S patterns).
No parameter schema in public metadata yet.
validate_cas_numberCAS registry check-digit validation.
CAS registry check-digit validation.
No parameter schema in public metadata yet.
convert_unitsMass, volume, energy, pressure, temperature, length, amount.
Mass, volume, energy, pressure, temperature, length, amount.
No parameter schema in public metadata yet.
lookup_periodic_tableZ, mass, electron config, electronegativity, radius, group.
Z, mass, electron config, electronegativity, radius, group.
No parameter schema in public metadata yet.
calculate_buffer_phHenderson-Hasselbalch solver with built-in pKa database.
Henderson-Hasselbalch solver with built-in pKa database.
No parameter schema in public metadata yet.
format_citationDOI to formatted reference in 20+ styles.
DOI to formatted reference in 20+ styles.
No parameter schema in public metadata yet.
build_bibliographyBatch DOIs to numbered, styled reference list.
Batch DOIs to numbered, styled reference list.
No parameter schema in public metadata yet.
lookup_iupac_nameSMILES to IUPAC systematic name.
SMILES to IUPAC systematic name.
No parameter schema in public metadata yet.
name_to_smilesCommon name to SMILES + InChI + InChIKey + MW.
Common name to SMILES + InChI + InChIKey + MW.
No parameter schema in public metadata yet.
format_molecular_formulaFormat molecular formula as Unicode, LaTeX, or HTML.
Format molecular formula as Unicode, LaTeX, or HTML.
No parameter schema in public metadata yet.
lookup_experimental_template18 reaction templates with fill-in fields and safety notes.
18 reaction templates with fill-in fields and safety notes.
No parameter schema in public metadata yet.
lookup_journal_guideSubmission requirements for 12 top chemistry journals.
Submission requirements for 12 top chemistry journals.
No parameter schema in public metadata yet.
generate_si_checklistSI checklist tailored to compound type.
SI checklist tailored to compound type.
No parameter schema in public metadata yet.
lookup_abbreviation193 standard abbreviations (solvents, reagents, spectroscopy).
193 standard abbreviations (solvents, reagents, spectroscopy).
No parameter schema in public metadata yet.
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RXN_API_KEYsecretIBM RXN key for retrosynthesis (free)
ROWAN_API_KEYsecretRowan key for pKa/NMR predictions (free)
Readme
🧪 labmate-mcp
Your AI lab companion — from literature search to benchwork to publication.
81 tools · 25+ scientific APIs · 202 named reactions · zero config required
Quick Start ↓ • What Can I Do? • All 81 Tools • Configuration • Examples
Details
- Repository
- github.com/jonasrackl/labmate-mcp
- Package
labmate-mcp- Transport
- STDIO
- Auth
- Required
- Registry
- MCP registry, active