https://github.com/JonasRackl/labmate-mcp
Your AI lab companion — 78 MCP tools for literature, compounds, synthesis, benchwork, peptides & publication writing
https://github.com/JonasRackl/labmate-mcp
ai-assistant bibtex chemistry citation-formatting claude crossref literature-search llm-tools mass-spectrometry mcp named-reactions nist openalex organic-chemistry pdb peptide pubchem retrosynthesis scientific-research semantic-scholar
Last synced: 27 days ago
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Your AI lab companion — 78 MCP tools for literature, compounds, synthesis, benchwork, peptides & publication writing
- Host: GitHub
- URL: https://github.com/JonasRackl/labmate-mcp
- Owner: JonasRackl
- License: mit
- Created: 2026-02-02T09:00:23.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2026-02-02T22:08:50.000Z (4 months ago)
- Last Synced: 2026-02-03T01:24:51.890Z (4 months ago)
- Topics: ai-assistant, bibtex, chemistry, citation-formatting, claude, crossref, literature-search, llm-tools, mass-spectrometry, mcp, named-reactions, nist, openalex, organic-chemistry, pdb, peptide, pubchem, retrosynthesis, scientific-research, semantic-scholar
- Language: Python
- Homepage: https://github.com/JonasRackl/labmate-mcp#-quick-start
- Size: 286 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
- awesome-mcp-security - labmate-mcp - 78 MCP tools for literature, compounds, synthesis, be... | 71 ⚠️ | - | [表示](https://agentseal.org/mcp/labmate-mcp) | (カテゴリ / 🔍 <a name="search--knowledge"></a>検索・ナレッジ)
README
# 🧪 labmate-mcp
**Your AI lab companion — from literature search to benchwork to publication.**
[](https://pypi.org/project/labmate-mcp/)
[](https://pypi.org/project/labmate-mcp/)
[](https://python.org)
[](LICENSE)
**81 tools** · **25+ scientific APIs** · **202 named reactions** · **zero config required**
[**Quick Start ↓**](#-quick-start) • [What Can I Do?](#-what-can-i-do-with-this) • [All 81 Tools](#-tool-reference) • [Configuration](#%EF%B8%8F-configuration) • [Examples](#-examples)
---
labmate-mcp is an [MCP server](https://modelcontextprotocol.io) that connects Claude to scientific databases, computational chemistry tools, bench references, and writing utilities. **One install covers the entire research workflow.**
📚 Literature
15 tools
⚗️ Synthesis
11 tools
🧪 Bench
30 tools
📊 Analysis
15 tools
✍️ Publication
10 tools
Search papers
Citation graphs
Author profiles
Preprints
Open access PDFs
Retrosynthesis
Forward prediction
Atom mapping
pKa / ADMET
NMR prediction
Named reactions
Reagent calculator
Protecting groups
Solvent reference
Rxn dev checklist
Isotope patterns
Mass spectra
Binding data
Crystal structures
Safety data
Format citations
Build bibliography
Experimental templates
Journal guides
SI checklist
## 🚀 Quick Start
```bash
pip install labmate-mcp
```
Then add this to your Claude config:
Claude Desktop → claude_desktop_config.json
On macOS: `~/Library/Application Support/Claude/claude_desktop_config.json`
On Windows: `%APPDATA%\Claude\claude_desktop_config.json`
```json
{
"mcpServers": {
"labmate": {
"command": "labmate-mcp"
}
}
}
```
Claude Code → .mcp.json in your project root
```json
{
"mcpServers": {
"labmate": {
"command": "labmate-mcp"
}
}
}
```
Docker
```bash
docker build -t labmate-mcp .
docker run -it labmate-mcp
```
Restart Claude. **61 of 81 tools work out of the box** — no API keys needed.
> [!TIP]
> Want retrosynthesis, pKa prediction, or NMR shifts? Run `labmate-mcp --setup` to add free API keys.
---
## 💬 What Can I Do With This?
Just talk to Claude naturally:
> **"Find the most cited papers on copper-catalyzed C–H activation from the last 5 years"**
Searches across multiple databases, ranks by citations, and gives you abstracts and AI-generated summaries.
> **"Suzuki coupling, 150 mg aryl bromide (MW 261), 5 mol% Pd(PPh₃)₄, 1.3 eq boronic acid, 2.5 eq K₂CO₃ — how much of everything?"**
Calculates exact masses for each reagent with your substrate as the limiting reagent.
> **"I'm developing a new reaction. What should I be thinking about?"**
Walks you through a structured [reaction development checklist](https://doi.org/10.1039/D4CS01046A) — covering everything from initial mechanistic hypotheses to scope exploration and scale-up.
> **"I need to protect a primary amine — stable to acid, cleavable by hydrogenation"**
Compares protecting groups against a stability matrix and suggests the best match (here: Cbz).
> **"Format these DOIs as an ACS bibliography, then give me an experimental template for a Buchwald–Hartwig"**
Generates a numbered reference list and a fill-in-the-blank procedure with suggested workup and safety notes.
More things you can ask
| Ask Claude… | What happens |
|:---|:---|
| "What are the NMR solvent peaks for DMSO-d₆?" | Residual ¹H: 2.50 ppm (quintet), ¹³C: 39.52 ppm, water: 3.33 ppm |
| "Generate 20 cyclic pentapeptides with some D-amino acids" | Returns SMILES with MW, logP, and TPSA for each |
| "I want to submit to JACS — what do I need to know?" | Word limits, abstract length, citation format, graphical abstract specs |
| "Retrosynthesis of ibuprofen" | Multi-step route back to commercial starting materials |
| "pKa of 4-nitrophenol?" | Quantum-chemistry prediction via Rowan Science |
| "Cooling bath for −42 °C?" | MeCN / dry ice, or chlorobenzene / dry ice |
---
## 🔧 Tool Reference
### 📚 Literature & Discovery — 15 tools
Search papers across multiple databases, explore citation graphs, find open access PDFs, and track research trends.
Show all 15 tools
| Tool | Source | What it does |
|:-----|:-------|:-------------|
| `search_papers` | Crossref + OpenAlex + S2 | Multi-source paper search with metadata fusion |
| `get_paper_details` | Crossref + OpenAlex + S2 | Full metadata: abstract, authors, citations, references |
| `find_similar_papers` | Semantic Scholar | Content-based paper recommendations |
| `get_paper_citations` | Semantic Scholar | Forward citation graph + context snippets |
| `get_paper_references` | Semantic Scholar | Backward citation graph (bibliography) |
| `get_author_profile` | OpenAlex + S2 | h-index, publications, co-authors, topics |
| `analyze_research_topic` | OpenAlex | Publication volume trends over time |
| `find_open_access_pdf` | Unpaywall | Legal open access PDF URLs |
| `search_chemrxiv` | Crossref + OpenAlex | Chemistry preprint search |
| `get_chemrxiv_categories` | — | List ChemRxiv subject categories |
| `search_web_of_science` | Web of Science | WoS search *(requires API key)* |
| `generate_bibtex` | Crossref | DOI → BibTeX (single or batch) |
| `get_journal_metrics` | OpenAlex | Impact metrics, open access %, policy |
| `search_protein_structures` | RCSB PDB | Search PDB by keyword, organism, method |
| `get_protein_structure` | RCSB PDB | Full PDB entry: resolution, ligands, sequence |
### 🔬 Compound Data & Safety — 12 tools
Look up any compound by name, SMILES, or formula. Get safety data, binding affinities, crystal structures, and more.
Show all 12 tools
| Tool | Source | What it does |
|:-----|:-------|:-------------|
| `search_compound` | PubChem | Name/SMILES/formula → compound data |
| `get_compound_properties` | PubChem | MW, SMILES, InChI, formula, XLogP, TPSA |
| `profile_compound` | Multiple | Comprehensive profile combining several databases |
| `get_safety_data` | PubChem GHS | GHS pictograms, H-statements, P-statements |
| `translate_compound_ids` | UniChem | Convert PubChem ↔ ChEMBL ↔ DrugBank ↔ ChEBI |
| `search_crystal_structures` | COD | Crystallography Open Database search |
| `search_materials_project` | Materials Project | Band gaps, formation energies *(requires key)* |
| `search_nist_webbook` | NIST | ΔHf, Cp, phase transitions, IR spectra |
| `search_mass_spectra` | MassBank | Mass spectrum search by exact mass or name |
| `search_binding_data` | BindingDB | IC₅₀, Ki, Kd binding affinities |
| `search_toxicity` | EPA CompTox | Toxicity endpoints *(requires key)* |
| `classify_natural_product` | GNPS | NP superclass / class / pathway |
### ⚗️ Computational Chemistry — 11 tools
AI-powered retrosynthesis, forward reaction prediction, pKa, solubility, ADMET, and NMR shift prediction.
Show all 11 tools
| Tool | Source | What it does |
|:-----|:-------|:-------------|
| `predict_retrosynthesis` | IBM RXN | Multi-step retrosynthetic analysis |
| `plan_synthesis` | IBM RXN | Forward synthesis route planning |
| `predict_product` | IBM RXN | Predict products from reactants + reagents |
| `predict_atom_mapping` | IBM RXN | Atom-by-atom mapping for mechanisms |
| `text_to_procedure` | IBM RXN | Natural language → structured procedure |
| `predict_pka` | Rowan Science | pKa values (any functional group, aqueous) |
| `predict_solubility` | Rowan Science | Aqueous solubility prediction |
| `predict_admet` | Rowan Science | Absorption, metabolism, toxicity prediction |
| `search_tautomers` | Rowan Science | Enumerate tautomeric forms |
| `compute_descriptors` | Rowan Science | Molecular descriptors from SMILES |
| `predict_nmr` | Rowan Science | ¹H and ¹³C chemical shift prediction |
*IBM RXN and Rowan tools require free API keys. See [Configuration](#%EF%B8%8F-configuration).*
### 🧬 Peptide Chemistry — 10 tools
Sequence-to-SMILES conversion with 450+ amino acids, cyclization, library generation, pI calculation, and MS/MS interpretation.
Show all 10 tools
| Tool | Source | What it does |
|:-----|:-------|:-------------|
| `peptide_to_smiles` | p2smi | Sequence → SMILES (450+ AAs, 5 cyclization types) |
| `peptide_cyclization_options` | p2smi | Which cyclizations does a sequence support? |
| `generate_peptide_library` | p2smi | Random peptide generation with NCAAs, D-stereo |
| `peptide_properties` | p2smi + RDKit | MW, logP, TPSA, HBD/HBA, Lipinski |
| `check_peptide_synthesis` | p2smi | SPPS feasibility: difficult motifs, aggregation |
| `modify_peptide` | p2smi | Apply N-methylation, PEGylation |
| `calculate_peptide_pi` | pichemist | Isoelectric point (8 pKa reference sets) |
| `calculate_peptide_extinction` | pep-calc.com | ε₂₈₀ (Trp/Tyr/Cys contributions) |
| `get_peptide_ion_series` | pep-calc.com | b/y/a/c/z ion ladders for MS/MS |
| `assign_peptide_ms_peaks` | pep-calc.com | Match m/z values to fragments |
### 🧪 Bench Chemistry — 18 tools
Everyday lab calculators and a reference library covering named reactions, protecting groups, solvents, workup protocols, and more.
Show all 5 calculators
| Tool | What it does |
|:-----|:-------------|
| `calculate_molarity` | Solve for any unknown: mass, moles, volume, or MW |
| `calculate_dilution` | C₁V₁ = C₂V₂ with automatic unit handling |
| `calculate_reaction_mass` | Multi-reagent mass calc from equivalents |
| `calculate_yield` | Percent yield from actual / theoretical |
| `calculate_concentration` | M ↔ mM ↔ mg/mL ↔ %w/v ↔ ppm ↔ ppb |
Show all 13 reference tools
| Tool | Coverage |
|:-----|:---------|
| `lookup_named_reaction` | **202 named reactions** — conditions, mechanism, scope, limitations |
| `lookup_rxn_dev_checklist` | Structured checklist for reaction development — [Kerr *et al.*, *Chem. Soc. Rev.* 2025](https://doi.org/10.1039/D4CS01046A) |
| `lookup_protecting_group` | **30 PGs** for OH, NH, C=O, COOH with stability / lability matrix |
| `lookup_workup_procedure` | Step-by-step protocols: LAH quench, aqueous extraction, etc. |
| `lookup_solvent_properties` | **32 solvents** — bp, density, polarity index, dielectric, miscibility |
| `lookup_cooling_bath` | **24 recipes** from −196 °C (lN₂) to +100 °C |
| `lookup_tlc_stain` | **13 stains** organized by functional group selectivity |
| `lookup_column_chromatography` | Solvent selection, Rf rules, loading, troubleshooting |
| `lookup_buffer_recipe` | **20+ buffers** — PBS, Tris, HEPES, TAE, TBE, RIPA, citrate… |
| `lookup_amino_acid_properties` | **20 canonical AAs** — MW, pKa, pI, hydropathy |
| `lookup_nmr_solvent` | **12 solvents** — residual ¹H/¹³C shifts, water peak, multiplicity |
| `lookup_lab_tips` | **35 practical tips** across 9 categories |
| `lookup_safety_card` | **9 safety cards** for hazardous reagents (*n*-BuLi, NaH, LAH…) |
### 🔧 Chemistry Utilities — 5 tools
Show all 5 tools
| Tool | What it does |
|:-----|:-------------|
| `calculate_isotope_pattern` | Isotope distribution from formula/SMILES (Cl, Br, S patterns) |
| `validate_cas_number` | CAS registry check-digit validation |
| `convert_units` | Mass, volume, energy, pressure, temperature, length, amount |
| `lookup_periodic_table` | Z, mass, electron config, electronegativity, radius, group |
| `calculate_buffer_ph` | Henderson-Hasselbalch solver with built-in pKa database |
### ✍️ Writing & Publication — 10 tools
Format citations, build bibliographies, generate experimental section templates, check journal requirements, and prepare your SI — all from within Claude.
Show all 10 tools
| Tool | Source | What it does |
|:-----|:-------|:-------------|
| `format_citation` | Crossref | DOI → formatted reference in **20+ styles** (ACS, RSC, Nature, Angew, APA…) |
| `build_bibliography` | Crossref | Batch DOIs → numbered, styled reference list |
| `lookup_iupac_name` | PubChem | SMILES → IUPAC systematic name |
| `name_to_smiles` | PubChem | Common name → SMILES + InChI + InChIKey + MW |
| `format_molecular_formula` | Local | C6H12O6 → C₆H₁₂O₆ (Unicode) / `\ce{C6H12O6}` (LaTeX) / `` (HTML) |
| `lookup_experimental_template` | Local | **18 reaction templates** with fill-in fields and safety notes |
| `lookup_journal_guide` | Local | Submission requirements for **12 top chemistry journals** |
| `generate_si_checklist` | Local | SI checklist tailored to compound type |
| `lookup_abbreviation` | Local | **193 standard abbreviations** (solvents, reagents, spectroscopy) |
| `get_thesis_guide` | Local | Section-by-section writing guide: abstract → SI |
---
## 📖 Examples
### Literature workflow
```
You: "Find the 5 most cited papers on photoredox catalysis from 2020–2024"
Claude: [returns papers ranked by citations with abstracts and TLDRs]
You: "Who cited paper #2? What topics did they focus on?"
Claude: [shows forward citation graph with context snippets]
You: "Is there a free PDF for paper #3?"
Claude: [finds a legal open access link via Unpaywall]
You: "Generate BibTeX for all 5"
Claude: [outputs formatted BibTeX entries]
```
### Synthesis planning
```
You: "I want to make 4-methoxybiphenyl from 4-bromoanisole"
Claude: [suggests Suzuki coupling, gives conditions and literature precedent]
You: "Calculate amounts for a 200 mg scale, 5 mol% catalyst"
Claude: [returns exact mg for every reagent and solvent volume]
You: "What's a good workup?"
Claude: [aqueous workup protocol with solvent, drying agent, and column conditions]
```
### Reaction development
```
You: "I have a new C–H activation — how do I figure out the mechanism?"
Claude: [suggests KIE, radical clocks, Hammett, Stern–Volmer, and computational approaches]
You: "Walk me through optimisation"
Claude: [covers DoE vs one-variable-at-a-time, green metrics, solvent screening]
You: "How do I prove this is catalytic, not stoichiometric?"
Claude: [mercury drop test, hot filtration, TON benchmarks, nonlinear effects]
```
### Writing a paper
```
You: "Format these 12 DOIs as an ACS bibliography"
Claude: [numbered reference list in ACS style]
You: "Give me an experimental template for a Sonogashira"
Claude: [fill-in-the-blank procedure with safety notes]
You: "What SI do I need for a small molecule paper?"
Claude: [checklist with ¹H/¹³C NMR, HRMS, mp, HPLC, formatting tips]
You: "I'm submitting to Angew — what are the requirements?"
Claude: [word limits, abstract format, citation style, graphical abstract specs]
```
---
## ⚙️ Configuration
The easiest way to add API keys:
```bash
labmate-mcp --setup
```
This walks you through each key and saves them to `~/.labmate-mcp.env`. They're loaded automatically whenever you use labmate.
**All keys are optional.** 61 of 81 tools work without any configuration.
Available API keys
| Variable | Service | Free? | What it unlocks |
|:---------|:--------|:-----:|:----------------|
| `RXN_API_KEY` | [IBM RXN](https://rxn.res.ibm.com) | ✅ | Retrosynthesis, product prediction, atom mapping |
| `ROWAN_API_KEY` | [Rowan Science](https://rowan.ai) | ✅ | pKa, solubility, ADMET, tautomers, NMR prediction |
| `SEMANTIC_SCHOLAR_API_KEY` | [Semantic Scholar](https://www.semanticscholar.org/product/api#api-key) | ✅ | Higher rate limits for citations & recommendations |
| `UNPAYWALL_EMAIL` | [Unpaywall](https://unpaywall.org/) | ✅ | Open access PDF discovery |
| `MATERIALS_PROJECT_API_KEY` | [Materials Project](https://materialsproject.org) | ✅ | Crystal structures, band gaps, formation energies |
| `WOS_API_KEY` | [Web of Science](https://developer.clarivate.com) | 🏛️ | Web of Science search (institutional) |
| `COMPTOX_API_KEY` | [EPA CompTox](mailto:ccte_api@epa.gov) | ✅ | Toxicity & environmental data |
**Aliases:** `S2_API_KEY`, `MP_API_KEY`, `RXN4CHEMISTRY_API_KEY` also work.
Manual configuration
If you prefer to configure keys manually, add them to your Claude config:
```json
{
"mcpServers": {
"labmate": {
"command": "labmate-mcp",
"env": {
"RXN_API_KEY": "your-rxn-key",
"ROWAN_API_KEY": "your-rowan-key",
"UNPAYWALL_EMAIL": "you@university.edu"
}
}
}
}
```
Or create `~/.labmate-mcp.env` directly:
```bash
RXN_API_KEY=your-rxn-key
ROWAN_API_KEY=your-rowan-key
```
---
## 🗄️ Built-in Databases
Everything below ships with labmate — no API calls, no internet required.
| | Database | Entries | What's inside |
|:--|:---------|-------:|:--------------|
| ⚗️ | Named reactions | **202** | Conditions, mechanism type, scope, limitations |
| 📋 | Rxn dev checklist | **30** questions | Kinetics, mechanism, DoE, catalysis, scope, scale-up |
| 🛡️ | Protecting groups | **30** | OH / NH / C=O / COOH, stability matrix |
| 🧴 | Solvents | **32** | bp, density, polarity index, dielectric, miscibility |
| ❄️ | Cooling baths | **24** | Recipes from −196 °C to +100 °C |
| 🎨 | TLC stains | **13** | Selectivity by functional group, recipe, procedure |
| 🧫 | Buffer recipes | **20+** | Preparation at specific pH, temperature correction |
| 🧬 | Amino acids | **20** | pKa, pI, MW, hydropathy, special notes |
| 📻 | NMR solvents | **12** | Residual ¹H, ¹³C, water peak, multiplicity |
| 📝 | Experimental templates | **18** | Fill-in-the-blank for common reaction types |
| 📰 | Journal guides | **12** | JACS, Angew, Nature Chem, JOC, Org Lett… |
| 🔤 | Abbreviations | **193** | Standard abbreviations across 7 categories |
| 💡 | Lab tips | **35** | Practical tips in 9 categories |
| ☣️ | Safety cards | **9** | Hazardous reagent protocols |
| 📄 | SI requirements | **18** | Per-technique formatting and common mistakes |
| 🎓 | Thesis writing | **6** | Section-by-section guidance |
All 202 named reactions
Alder-Ene · Aldol · Appel · Arbuzov · Arndt-Eistert · Baeyer-Villiger · Balz-Schiemann · Bamford-Stevens · Barton Decarboxylation · Barton-McCombie · Baylis-Hillman · Beckmann · Biginelli · Birch · Bischler-Napieralski · Blanc Chloromethylation · Bouveault-Blanc · Brown Hydroboration · Buchner Ring Expansion · Buchwald-Hartwig (C–N) · Buchwald-Hartwig (C–O) · Burgess Dehydration · Cadiot-Chodkiewicz · Cannizzaro · Carroll · Catellani · CBS · Chan-Lam · Chichibabin · Claisen Condensation · Claisen Rearrangement · Clemmensen · Click (CuAAC) · Comins · Cope Elimination · Cope Rearrangement · Corey-Bakshi-Shibata · Corey-Chaykovsky · Corey-Fuchs · Corey-Kim · Corey-Nicolaou · Corey-Winter · Cross-Metathesis · Curtius · Dakin · Darzens · Dess-Martin · Dieckmann · Diels-Alder · Doering-LaFlamme · Enders SAMP/RAMP · Eschenmoser-Claisen · Eschenmoser-Tanabe Fragmentation · Eschweiler-Clarke · Evans Aldol · Favorskii · Ferrier · Finkelstein · Fischer Esterification · Fischer Indole · Fleming-Tamao · Friedel-Crafts Acylation · Friedel-Crafts Alkylation · Fries · Fukuyama · Gabriel · Gewald · Glaser · Grignard · Grubbs Metathesis · Hantzsch Pyridine · Heck · Henry · Hiyama · Hiyama-Denmark · Hofmann · Horner · Horner-Wadsworth-Emmons · IBX · Ireland-Claisen · Jacobsen Epoxidation · Jones · Julia-Lythgoe · Kharasch · Knoevenagel · Knorr Pyrrole · Koenigs-Knorr · Kolbe · Kulinkovich · Kumada · Lawesson · Lemieux-Johnson · Ley · Liebeskind-Srogl · Lossen · Luche · Malaprade · Mander Methylenation · Mannich · Matteson · Meerwein Arylation · Meerwein Reduction · Meerwein-Ponndorf-Verley · Meinwald · Michael · Midland · Minisci · Mitsunobu · Modified Julia · Mukaiyama Aldol · Myers · Negishi · Noyori · Nozaki-Hiyama-Kishi · Ohira-Bestmann · Olefin Metathesis · Oppenauer · Oppolzer Sultam · Overman · Oxy-Cope · Ozonolysis · Paal-Knorr · Parikh-Doering · Passerini · Paternò-Büchi · Pauson-Khand · Petasis · Peterson · Pfitzner-Moffatt · Piancatelli · Pictet-Spengler · Pinner · Pinnick · Polonovski · Prevost · Prins · Ramberg-Bäcklund · Reductive Amination · Reformatsky · Rieche · Riley · Ring-Closing Metathesis · Ritter · Robinson Annulation · Roskamp · Roush · Rubottom · Saegusa-Ito · Sakurai-Hosomi · Sandmeyer · Schmidt · Shapiro · Sharpless AD · Sharpless AE · Shi Epoxidation · Shiina · Simmons-Smith · Skraup · Sonogashira · Staudinger Ligation · Staudinger Reduction · Steglich · Stetter · Still-Gennari · Stille · Stork Enamine · Strecker · Suzuki · Suzuki-Miyaura · Swern · Takai · Tebbe · TEMPO · Tiffeneau-Demjanov · Transfer Hydrogenation · Trost AAA · Tsuji-Trost · Ugi · Ullmann · Upjohn · Van Leusen · Vilsmeier-Haack · Wacker · Weinreb Amide · Wharton · Williamson · Wittig · Wittig Rearrangement · Wohl-Ziegler · Wolff · Wolff-Kishner · Yamaguchi · Zincke Aldehyde
Reaction development checklist — 7 sections
Based on Kerr, Jenkinson, Sheridan & Sparr, "Reaction Development: A Student's Checklist", [*Chem. Soc. Rev.* 2025, DOI: 10.1039/D4CS01046A](https://doi.org/10.1039/D4CS01046A). Each section contains guiding questions, specific checks to perform, and practical tips.
| Section | Questions |
|:--------|----------:|
| 🔍 Take Stock | 5 |
| 📈 Kinetics & Thermodynamics | 6 |
| ⚙️ Mechanism | 4 |
| 📊 Optimisation | 3 |
| 🔄 Catalysis | 4 |
| 🎯 Scope | 3 |
| 🚀 Applications | 5 |
| **Total** | **30** |
---
## 🏗️ Architecture
```
labmate_mcp/
├── server.py 5,248 lines 81 MCP tool definitions + response formatting
├── bench.py 4,714 lines Calculators + reference databases
├── apis.py 1,744 lines HTTP clients for 25+ scientific APIs
├── writing.py 1,488 lines Citations, templates, journal guides, SI, thesis
├── chemistry.py 572 lines Isotope patterns, CAS, units, periodic table, pH
├── peptide.py 384 lines p2smi + pichemist + pep-calc.com integration
└── __init__.py 4 lines Version
──────────────
14,154 lines
```
---
## 🤝 Contributing
Contributions are welcome! See [CONTRIBUTING.md](CONTRIBUTING.md) for details.
High-impact areas: more named reactions, more experimental templates, more journal guides, tests, and bug reports.
---
## 📄 License
[MIT](LICENSE) — use freely in academia and industry.
---
## 📚 Cite
If labmate-mcp is useful in your research, please cite the tools it builds on:
- **Reaction development checklist** — Kerr, M. A.; Jenkinson, M. A.; Sheridan, H.; Sparr, C. *Chem. Soc. Rev.* **2025**. [doi:10.1039/D4CS01046A](https://doi.org/10.1039/D4CS01046A)
- **p2smi** — Feller, A. *JOSS* **2025**, *10*, 8319. [doi:10.21105/joss.08319](https://doi.org/10.21105/joss.08319)
- **pichemist** — Trastoy, B. *et al.* *J. Chem. Inf. Model.* **2023**. [AstraZeneca/peptide-tools](https://github.com/AstraZeneca/peptide-tools)
- **OpenAlex** — Priem, J.; Piwowar, H.; Orr, R. [arXiv:2205.01833](https://arxiv.org/abs/2205.01833) (2022)
Made with 🧪 for chemists who'd rather be in the lab than Googling.