Labmate MCP server

Read from the package source without running it. The installed server may list more.

• analyze_research_topic

  Analyze publication trends for a research topic. Returns: - Publication volume per year - Top authors in the field - Top journals publishing on this topic - Open access proportion

• assign_peptide_ms_peaks

  Assign observed m/z peaks to peptide deletions, modifications, or fragment ions using pep-calc.com. Helps identify impurities, truncations, and post-translational modifications in MALDI/ESI-MS data.

• build_bibliography

  Build a formatted bibliography from a list of DOIs. Outputs a numbered reference list in the specified style (ACS, APA, Nature, etc.). Ideal for thesis chapters, manuscript reference sections, and literature reviews.

• calculate_buffer_ph

  Henderson-Hasselbalch calculator. Two modes: (1) Given pKa + concentrations → calculate pH. (2) Given pKa + target pH → calculate required acid:base ratio. Knows pKa for 20+ common buffers: Tris (8.07), HEPES (7.55), phosphate (7.20), MOPS (7.20), MES (6.15), acetate (4.76), etc.

• calculate_concentration

  Convert between concentration units (M, mM, μM, mg/mL, %w/v, ppm, ppb, etc.). MW required for molar↔mass conversions.

• calculate_dilution

  C₁V₁ = C₂V₂ dilution calculator. Provide any 3 values → solves for the 4th. Reports solvent to add.

• calculate_isotope_pattern

  Calculate theoretical isotope distribution from molecular formula or SMILES. Returns monoisotopic mass, average mass, and isotope envelope (m/z + relative abundance). Essential for mass spec data interpretation, especially for compounds containing Cl, Br, S.

• calculate_molarity

  Calculate molarity/concentration. Provide 2-3 knowns (mass, moles, volume, MW, formula) → solves for unknowns. Handles M=n/V, n=m/MW, and all permutations.

• calculate_peptide_extinction

  Calculate peptide properties via pep-calc.com: MW, formula, pI, charge summary, and extinction coefficient at 280nm (oxidized/reduced). Supports 120+ amino acids including phospho-residues. Free API, no key required.

• calculate_peptide_pi

  Calculate peptide isoelectric point (pI) using AstraZeneca's pichemist. Uses 8 different pKa reference sets (IPC2, ProMoST, Gauci, Grimsley, Thurlkill, Lehninger, Toseland) for consensus pI with error bars. Also returns charge at pH 7.4. Accepts FASTA sequence or SMILES (for modified peptides with noncanonical AAs).

• calculate_reaction_mass

  Calculate mass, moles, and volume for each reagent in a reaction. Specify one limiting reagent with known mass/moles, set equivalents for others → get required amounts for all.

• calculate_yield

  Calculate percent yield. Provide actual product amount and either theoretical amount or limiting reagent info.

• check_peptide_synthesis

  Evaluate solid-phase peptide synthesis (SPPS) feasibility. Checks: forbidden motifs (consecutive Pro, DG/DP, N/Q at N-term), cysteine overload, C-terminal Pro/Cys, glycine runs, length limits, hydrophobicity, and charge distribution.

• classify_natural_product

  Classify a compound into natural product categories using GNPS NPClassifier. Returns biosynthetic pathway, superclass, and class predictions. Uses ML models trained on natural product structural features. No authentication required.

• compute_descriptors

  Compute molecular descriptors using Rowan Science. Returns cheminformatics descriptors computed from the molecular structure.

• convert_units

  Convert between scientific units. Supports: mass (g↔mg↔μg↔Da↔kDa), volume (L↔mL↔μL), length (m↔nm↔Å↔pm), energy (J↔kJ↔kcal↔kcal/mol↔kJ/mol↔eV↔hartree↔cm⁻¹), pressure (Pa↔atm↔bar↔torr↔mmHg), time (s↔ms↔μs↔ns↔min↔h), amount (mol↔mmol↔μmol), temperature (°C↔°F↔K).

• find_open_access_pdf

  Find a free, legal PDF for a paper using Unpaywall. Returns direct PDF link, OA status (gold/green/hybrid/bronze), and the repository or publisher hosting it.

• find_similar_papers

  Find papers similar to a given paper using Semantic Scholar's recommendation engine. Based on citation patterns and content similarity. Returns papers with TLDRs and citation counts.

• format_citation

  Format a DOI into a properly styled citation. Styles: ACS (default), APA 7th, Nature, Vancouver, Chicago, MLA, BibTeX. Uses Crossref content negotiation for authoritative metadata. Essential for manuscripts, theses, and reference lists.

• format_molecular_formula

  Format a molecular formula with proper subscript notation. Outputs in Unicode (C₆H₁₂O₆), LaTeX (\ce{C6H12O6}), HTML (₆), or all formats. Handles complex formulae including parentheses and charges. Essential for manuscripts, theses, and presentations.

• generate_bibtex

  Generate BibTeX entries from DOIs for use in LaTeX/BibTeX. Uses Crossref content negotiation — works for any DOI in Crossref. Supports batch: pass multiple DOIs separated by commas.

• generate_peptide_library

  Generate random peptide sequences with controlled properties. Supports noncanonical amino acids (100+ from SwissSidechain), D-stereochemistry, and 5 cyclization types. Useful for library design and computational peptide chemistry.

• generate_si_checklist

  Generate a Supporting Information (SI) checklist for a chemistry publication. Tailored to compound type (small molecule, peptide, polymer, material, natural product). Lists required characterization data, formatting guidelines, and common reviewer complaints. Saves time during submission preparation.

• get_author_profile

  Look up an author's profile including h-index, citation count, publication history, and institutional affiliation. Searches both Semantic Scholar and OpenAlex for comprehensive coverage.

• get_chemrxiv_categories

  List all ChemRxiv subject categories.

• get_compound_properties

  Get detailed computed molecular properties from PubChem. Includes Lipinski rule-of-5 parameters, TPSA, XLogP, and all common names.

• get_journal_metrics

  Look up journal metrics including h-index, citation statistics, open access percentage, and publication counts. Data from OpenAlex (free, no authentication required).

• get_paper_citations

  Get papers that cite a given work. Includes influence scores and citation intents (methodology, background, result comparison). Uses Semantic Scholar's citation graph.

• get_paper_details

  Get comprehensive details for a paper by DOI. Aggregates data from Crossref (metadata), OpenAlex (abstract, topics, citations), Semantic Scholar (TLDR, influence), and Unpaywall (open access PDF).

• get_paper_references

  Get the reference list of a paper with influence analysis. Shows which references are influential (key vs. background citations). Uses Semantic Scholar's citation graph.

• get_peptide_ion_series

  Get peptide MS/MS fragment ion series (b, y, a, c, z ions) for tandem mass spectrometry interpretation. Returns theoretical m/z values for each ion type at every cleavage position. Essential for de novo sequencing and spectral annotation.

• get_protein_structure

  Get full details for a specific PDB structure including method, resolution, chains, ligands, and primary citation.

• get_safety_data

  Get GHS hazard classification for a chemical compound. Returns signal word, hazard pictograms, H-statements, and P-statements. Data from PubChem's GHS classification records.

• get_thesis_guide

  Get writing guidance for each section of a chemistry thesis or dissertation. Covers: introduction, literature review, methods/experimental, results, discussion, conclusion, abstract, and acknowledgements. For each section: purpose, structure, writing tips, and common mistakes to avoid.

• lookup_abbreviation

  Look up chemistry abbreviations and acronyms. 193 entries across 7 categories: solvents, reagents, protecting groups, techniques, units, spectroscopy, and general chemistry. Returns full expansion. Also accepts category names to list all abbreviations in that category. Essential for decoding literature and ensuring correct abbreviation usage in manuscripts.

• lookup_amino_acid_properties

  Look up amino acid properties: MW (residue), pKa values (α-carboxyl, α-amino, sidechain), pI, Kyte-Doolittle hydropathy index, structural class, and practical notes (UV absorption, phosphorylation, reactivity). Covers all 20 canonical amino acids.

• lookup_buffer_recipe

  Search 20+ common laboratory buffer recipes. Returns: exact recipe with masses, preparation steps, pH range, pKa, and practical notes. Covers: PBS, TBS, Tris, HEPES, MES, MOPS, PIPES, citrate, acetate, carbonate, TAE, TBE, SDS-PAGE, transfer buffer, TE, RIPA lysis.

• lookup_column_chromatography

  Column chromatography guide. Search for: solvent selection, loading methods, Rf rules, troubleshooting (streaking, poor separation, compound stuck), gradient tips, fraction size, flow rate. Includes 8 common solvent systems.

• lookup_cooling_bath

  Find cooling bath recipes. Provide target temp → get recipe. Covers -196°C (liq N₂) to +100°C. Common: -78°C dry ice/acetone, -42°C MeCN/dry ice, 0°C ice/water, -15°C ice/NaCl.

• lookup_experimental_template

  Get a template for writing the Experimental section of a paper or thesis. Covers 18 common reaction types (cross-coupling, oxidation, reduction, heterocycle synthesis, etc.) with fill-in-the-blank templates that follow journal conventions. Each template includes: reaction setup, workup, purification, and characterization data format.

• lookup_iupac_name

  Convert a SMILES string to its IUPAC systematic name using PubChem. Returns the preferred IUPAC name along with any common synonyms. Useful for writing experimental sections and compound characterization.

• lookup_journal_guide

  Look up submission formatting guidelines for major chemistry journals. Covers 12 top journals (JACS, Angew. Chem., Nature Chemistry, JOC, Org. Lett., Chemical Science, etc.). Returns: citation style, word/page limits, figure requirements, SI guidelines, common mistakes, and submission tips.

• lookup_lab_tips

  Search practical lab tips and 'Law of the Lab' wisdom. 35 tips across 9 categories: reaction_setup (Grignard initiation, degassing, syringe technique, scale-up, molecular sieves), temperature_control (cooling baths, cryogenic technique, kinetic vs thermodynamic), moisture_sensitive (Schlenk line, solvent drying guide), workup_tips (breaking emulsions, drying agents, rotovap), purification_tips, an

• lookup_named_reaction

  Search 86+ named organic reactions. Returns conditions, mechanism, substrate scope, limitations, and related reactions. Covers: cross-couplings, oxidations, reductions, rearrangements, cycloadditions, FGIs, radical, heterocycle synthesis.

• lookup_nmr_solvent

  NMR solvent reference: residual ¹H and ¹³C chemical shifts, water peak position, multiplicity, boiling point, density. Covers: CDCl₃, DMSO-d₆, MeOD, D₂O, acetone-d₆, MeCN-d₃, C₆D₆, THF-d₈, CD₂Cl₂, DMF-d₇, pyridine-d₅, TFA-d. Essential for spectral interpretation and thesis writing.

• lookup_periodic_table

  Look up element properties from the periodic table: atomic number, atomic mass, electron configuration, electronegativity (Pauling), group, period, block, and category. Covers all commonly encountered elements in organic, inorganic, and materials chemistry.

• lookup_protecting_group

  Search 30 protecting groups across hydroxyl, amino, carbonyl, carboxyl. Returns protection/deprotection conditions and stability matrix (acid/base/nucleophile/oxidation/reduction/H₂-Pd). S=stable, M=moderate, L=labile.

• lookup_rxn_dev_checklist

  Search the Reaction Development Checklist — a comprehensive guide for methodology studies. Based on Kerr, Jenkinson, Sheridan & Sparr, Chem. Soc. Rev. 2025 (DOI: 10.1039/D4CS01046A). 7 sections with actionable questions and practical tips: Take Stock (product characterisation, mass balance, reproducibility, minimal retron), Kinetics & Thermodynamics (rate laws, driving forces, equilibrium), Mechan

• lookup_safety_card

  Look up hazardous reagent safety cards. 9 cards covering: n-BuLi, t-BuLi, LAH (LiAlH4), NaH, diazomethane (CH2N2), OsO4, HF, NaN3, Pd/C. Each card: hazards, handling protocol, quench procedure, first aid, storage. Essential quick-reference before working with dangerous reagents.

• lookup_solvent_properties

  Search 32 common lab solvents. Returns: boiling point, density, polarity index, dielectric constant, water miscibility, common uses, and safety notes.

• lookup_tlc_stain

  Search TLC stain recipes by functional group or stain name. Returns: recipe, preparation, visualization procedure, and which functional groups each stain detects. Covers: KMnO₄, CAM, ninhydrin, anisaldehyde, vanillin, DNP, PMA, Dragendorff, I₂, UV.

• lookup_workup_procedure

  Search bench workup procedures. Returns step-by-step protocols for: standard aqueous workup, acid-base extraction, Fieser (LAH/DIBAL), NH₄Cl quench, Rochelle's salt, and more.

• modify_peptide

  Apply N-methylation and/or PEGylation to a peptide SMILES. N-methylation improves metabolic stability and membrane permeability. PEGylation increases solubility and plasma half-life. Returns modified SMILES with validation.

• name_to_smiles

  Convert a compound name to its SMILES string using PubChem. Returns canonical and isomeric SMILES, InChI, InChIKey, molecular formula, and MW. Useful for quickly getting machine-readable structures from common names, trade names, or reagent labels.

• peptide_cyclization_options

  Check which cyclization types a peptide sequence supports. Analyzes residues for disulfide-capable (Cys), nucleophilic sidechain (Lys, Ser, etc.), and electrophilic sidechain (Asp, Glu, etc.) positions.

• peptide_properties

  Compute peptide molecular properties from SMILES: molecular weight, formula, logP, TPSA, H-bond donors/acceptors, rotatable bonds, ring count, fraction Csp3, heavy atoms, formal charge, and Lipinski Rule-of-5 evaluation.

• peptide_to_smiles

  Convert peptide sequence to SMILES. Supports 450+ amino acids (canonical + noncanonical from SwissSidechain), D-stereochemistry, and 5 cyclization types: disulfide, head-to-tail, sidechain-to-sidechain, sidechain-to-N-term, sidechain-to-C-term.

• plan_synthesis

  Turn a retrosynthetic route into a step-by-step synthesis procedure with actions. Chain this after predict_retrosynthesis to get a full synthesis plan.

• predict_admet

  Predict ADMET properties using Rowan Science. Computes absorption, distribution, metabolism, excretion, and toxicity predictions.

• predict_atom_mapping

  Map atoms from reactants to products using IBM RXN AI (atom-mapping-2020 model). Shows which atom in the reactants becomes which atom in the products.

• predict_nmr

  Predict ¹H and ¹³C NMR chemical shifts using Rowan Science. Uses conformer search + neural network potentials to predict NMR spectra.

• predict_pka

  Predict pKa values using Rowan Science quantum chemistry. Computes acid and base dissociation constants for any molecule from SMILES.

• predict_product

  Predict reaction product(s) from reactants using IBM RXN AI. The complement to retrosynthesis — give it starting materials and it predicts what you'll get.

• predict_retrosynthesis

  Predict retrosynthetic routes using IBM RXN for Chemistry. Uses transformer-based AI to plan multi-step synthesis pathways.

• predict_solubility

  Predict molecular solubility using Rowan Science. Supports aqueous and organic solvents using ML models.

• profile_compound

  Generate a comprehensive compound profile by querying all available databases. Combines: PubChem (structure, properties) + CAS (registry) + NIST WebBook (thermochemistry) + UniChem (cross-references) + GHS (safety data).

• search_binding_data

  Search BindingDB for quantitative binding affinities (Ki, IC50, Kd, EC50). 3.2 million measurements including patent-derived data. No authentication required.

• search_chemrxiv

  Search ChemRxiv chemistry preprints via Crossref. Enriches results with abstracts from OpenAlex.

• search_compound

  Search for chemical compounds by name, CAS number, SMILES, or formula. Returns structure information, identifiers, and basic properties.

• search_crystal_structures

  Search the Crystallography Open Database (COD) for experimental crystal structures. Returns space groups, cell parameters, and CIF file links. 500,000+ structures under CC0 license. No authentication required.

• search_mass_spectra

  Search MassBank EU for reference mass spectra (MS/MS). 120,000+ curated spectra from 18,500 compounds. Use for compound identification and spectral matching. No authentication required.

• search_materials_project

  Search Materials Project for inorganic materials with DFT-calculated properties. Returns band gaps, formation energies, stability, and crystal symmetry.

• search_nist_webbook

  Search the NIST Chemistry WebBook for thermochemical and physical property data. Returns melting/boiling points, enthalpies of formation/vaporization/fusion, heat capacities, entropies, and links to IR/MS/UV-Vis spectra.

• search_papers

  Search academic literature. Returns papers with titles, authors, citations, and AI-generated TLDRs.

• search_protein_structures

  Search the RCSB Protein Data Bank for experimental protein/nucleic acid structures. 230,000+ structures including X-ray, cryo-EM, and NMR. No authentication required.

• search_tautomers

  Enumerate and rank tautomers using Rowan Science. Uses quantum chemistry to identify all relevant tautomeric forms and rank them by energy.

• search_toxicity

  Search the EPA CompTox Dashboard for toxicity, environmental fate, and physicochemical property data. Contains 1.2M+ chemicals with ToxCast bioactivity screening and hazard classifications.

• search_web_of_science

  Search Web of Science for peer-reviewed literature.

• text_to_procedure

  Extract machine-readable steps from experimental text using IBM RXN NLP. Converts free-text experimental paragraphs into structured action sequences (MAKESOLUTION, ADD, STIR, FILTER, CONCENTRATE, etc.).

• translate_compound_ids

  Translate a compound's InChIKey to identifiers in 40+ databases. Links PubChem CID ↔ ChEMBL ID ↔ DrugBank ID ↔ ZINC ID ↔ CAS RN and more.

• validate_cas_number

  Validate a CAS registry number by checking the check digit. Returns whether the number is valid and the properly formatted CAS string. Useful for verifying catalog numbers and safety data lookup.

• Code scan11 source files scanned25/25
• –Live reliabilityno gateway calls yet and no remote to proben/a
• –Tool poisoningtools not inspected (local package is not executed); not countedn/a
• Auth qualitystatic API keys via environment variables6/15
• Maintenancelast push 237 days ago4/15
• Maintainer identityregistry namespace matches repository owner6/10

Safety score

63/100

higher than 18% of 48,255 servers

Tools

81

the typical server has 7

Tools that change things

0%

typical: 0%. Fewer write tools means less an agent can break

GitHub stars

3

more than 80% of 28,688 servers

Downloads a week

25

more than 11% of 12,191 servers with a package

Labmate: common questions

Is Labmate MCP server safe?

With care: it is graded C, so read the findings first (63/100). Read the Labmate safety report

How do I install Labmate?

It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.

Does Labmate need an API key?

Yes. The registry entry asks for RXN_API_KEY, ROWAN_API_KEY.

Is Labmate maintained?

The last commit was 274 days ago (2026-02-03). The latest release is v7.3.1.

How does Labmate compare with other MCP servers?

safety score 63/100 (higher than 18% of 48,255 servers); tools 81 (the typical server has 7); tools that change things 0% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.