Chemistry
Installable Claude components for cheminformatics, computational chemistry, chemical structure handling, reaction prediction, retrosynthesis, and chemistry-aware language interfaces.
ADMET Prediction (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that profiles a compound’s absorption, distribution, metabolism, excretion, and toxicity into a graded pass/warn/fail scorecard.
ADMETlab MCP Server
MCP server · ToxMCP (community) · Beta · verified: degraded · security: caution
Self-hostable MCP server wrapping the ADMETlab 3.0 API for molecule washing, SVG rendering, ADMET property prediction, and CSV retrieval.
ALKYL
Claude Code Plugin · Kyllian de Vos (community) · Beta · verified: works · security: caution
Claude Code plugin bundling 27 computational-chemistry skills — RDKit, docking, MD, quantum chemistry, free energy, generative design — plus four keyless MCP servers.
Adverse Outcome Pathway (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that maps chemicals to adverse outcome pathways using AOPWiki, GHS/IARC classification, LD50 data, and toxicogenomics.
Anthropic PubMed Connector
MCP server · Anthropic · GA · verified: works · security: cleared
Anthropic-managed NCBI literature search via PubMed and PubMed Central.
AutoDock Vina (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Molecular docking with AutoDock Vina (Python API).
BGPT Paper Search (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.
BLAST (Bio-MCP)
MCP server · Bio-MCP · GA · verified: works · security: caution
MCP server wrapping NCBI BLAST+ for nucleotide/protein similarity search and custom database creation, run locally over stdio.
Binder Discovery (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: caution
ToolUniverse agent skill that discovers small-molecule binders for a target via known-ligand mining, similarity expansion, docking, and ADMET filtering into a ranked shortlist.
BindingDB (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Measured protein–small-molecule binding affinities from BindingDB; a source in the Chemistry connector in Claude Science.
BioContextAI Knowledgebase MCP
MCP server · BioContextAI · GA · verified: works · security: cleared
Read-only MCP that unifies 14+ biomedical databases (Antibody Registry, UniProt, STRING, AlphaFold, KEGG, Open Targets) for immune and protein-context queries.
BioMCP
MCP server · GenomOncology · GA · verified: degraded · security: cleared
Unified biomedical lookup across PubMed, ClinicalTrials.gov, MyVariant, and OpenFDA.
BioPython (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Comprehensive molecular biology toolkit.
BioRender Connector
MCP server · BioRender · GA · verified: degraded · security: cleared
Scientific-figure assembly from the 50,000+ BioRender icon and template library.
BioServices (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Unified Python interface to 40+ bioinformatics services.
Biomni (Claude Skill)
Claude Skill · Stanford SNAP Lab · GA · verified: works · security: caution
General-purpose biomedical AI agent that plans and runs multi-step research workflows across genomics, drug discovery, and clinical analysis.
Boltz (Claude Code Plugin)
Claude Code Plugin · Boltz · GA · verified: works · security: caution
Skills that drive the hosted Boltz API to predict biomolecular structures, screen and design small molecules, and design protein/antibody binders.
CDXML Toolkit
MCP server · Hiu Fung Kevin Lee · Beta · verified: works · security: caution
MCP server that draws molecules and reaction schemes to publication-ready ChemDraw CDXML, parses ELN/LCMS/NMR files, and reads structures from images.
COBRApy (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill driving COBRApy for constraint-based metabolic modelling — FBA, FVA, gene knockouts, flux sampling, gapfilling on SBML genome-scale models.
ChEBI (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Chemical Entities of Biological Interest — curated small-molecule ontology and annotations; a source in the Chemistry connector in Claude Science.
ChEMBL Connector
Claude Code Plugin · EMBL-EBI (Anthropic-packaged) · GA · verified: works · security: cleared
Anthropic-packaged plugin and Claude.ai connector over EMBL-EBI’s ChEMBL bioactive-compound database — compound, target, bioactivity, and mechanism-of-action lookup.
ChemCP
MCP server · Scott Reed · GA · verified: works · security: caution
MCP App that renders interactive 2D molecular structures from SMILES and computes basic properties inside Claude conversations via RDKit.js.
ChemGraph
MCP server · Argonne National Laboratory (ALCF) · Beta · verified: works · security: cleared
Argonne MCP server that runs real molecular simulations through ASE — geometry optimization, energies, and frequencies via xTB, DFT, or ML potentials.
ChemLint
MCP server · molML (TU/e) · GA · verified: works · security: cleared
MCP server exposing 150+ molecular machine-learning tools — SMILES cleaning, descriptors, similarity, clustering, model training — so Claude runs cheminformatics ML without Python scripting.
Chemical Safety (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill for chemical hazard and toxicology assessment via ADMET-AI, CTD toxicogenomics, AOPWiki, GHS/IARC classification, and regulatory safety data.
Chemical Sourcing (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that finds commercial suppliers for a compound across ZINC, Enamine, eMolecules, and Mcule, with purchasable-analog fallback.
Composer
Plugin · Scripps AI Enablement · Beta · verified: works · security: cleared
Turns a plain-language scientific problem into a grounded, runnable Claude solution composed from this catalog, reusing recipes and, for open-ended goals, assembling a multi-agent system from those same components.
Consensus Plugin
Claude Code Plugin · Consensus · GA · verified: degraded · security: cleared
Consensus.app MCP plugin bringing AI-powered scientific literature search and evidence synthesis into Claude across all research areas.
CovaSyn Chemistry MCP
MCP server · CovaSyn · GA · verified: degraded · security: caution
Hosted deterministic cheminformatics MCP with 130+ tools spanning ADMET, docking, retrosynthesis, ICH M7 toxicology, NMR/MS, and biologics design.
Database Lookup (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs.
Datamol (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill wrapping Datamol — an RDKit-based Python library for molecular standardization, transformations, featurization, and parallel processing on large compound libraries.
DeepChem (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill driving DeepChem for molecular machine learning — graph neural nets (GCN, GAT, MPNN, AttentiveFP), featurization, and the MoleculeNet benchmarks (toxicity, ADMET, quantum properties).
Dose-Response Analysis (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that fits four-parameter logistic curves to concentration-response data, returning IC50/EC50, Hill slope, Emax, and fit quality.
DrugBank MCP Server
MCP server · openpharma-org (community) · GA · verified: works · security: caution
Community MCP server exposing a local DrugBank SQLite (17k+ drugs) with 16 query methods for repurposing, target lookup, interactions, and structural similarity.
EMBL-EBI OLS (Claude Skill)
Claude Skill · Google DeepMind · GA · verified: degraded · security: cleared
Resolve and navigate biomedical ontology terms (GO, MONDO, HP, CHEBI, CL, UBERON, EFO, …) across 250+ ontologies via the EMBL-EBI Ontology Lookup Service.
Enzyme Kinetics (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA
ToolUniverse agent skill that fits Michaelis-Menten kinetics to substrate-velocity data and classifies inhibition mechanism with a Ki estimate.
Gene Ontology MCP Server
MCP server · Augmented Nature · Beta · verified: works · security: caution
Query GO terms, annotations, and enrichment inputs from the Gene Ontology; part of the Genes & Ontologies connector in Claude Science.
GlyGen MCP Server
MCP server · GlyGen · Beta · verified: degraded · security: caution
First-party remote MCP server over GlyGen’s integrated glycan, glycoprotein, biomarker, and disease data — protein, site, glycan, biomarker, and disease summaries.
Guide to Pharmacology (GtoPdb) (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and approved drugs.
Hypothesis Crucible (Claude Plugin)
Claude Plugin · Scripps AI Enablement · GA · verified: works · security: cleared
Agentic cross-corpus hypothesis generation — mines typed knowledge fragments from literature, structured databases, and raw experimental data, bridges them Swanson-style into novel connections, then runs a falsification gauntlet that aggressively rejects non-novel, ungrounded, contradicted, or implausible ideas, emitting only survivors with cited support and a discriminating experimental test.
Hypothesis Generation (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Structured hypothesis formulation from observations.
Inductive Bio ADMET Connector
Claude.ai Connector · Inductive Bio · GA · verified: degraded · security: cleared
Claude.ai connector surfacing Inductive Bio’s ADMET prediction models so drug-discovery chemists can predict compound properties in-conversation.
Ketcher Chemistry (Claude Science Connector)
Claude.ai Connector · EPAM Systems · GA · verified: works · security: cleared
Interactive 2D molecule sketcher (Ketcher) for drawing/editing chemical structures; the Ketcher Chemistry connector in Claude Science.
LabMate MCP
MCP server · Jonas Rackl · GA · verified: works · security: caution
One-install cheminformatics MCP with 81 tools — retrosynthesis, forward/ADMET/pKa/NMR prediction, 202 named reactions, reagent calculators, compound and literature lookup.
Literature Review (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).
MedChem (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill wrapping MedChem — drug-likeness filters (Lipinski, Veber, Egan, Muegge), ADMET-flag detection, and medicinal-chemistry alerts on top of RDKit.
MetaboLights (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Metabolomics studies, metadata, and metabolite data from EMBL-EBI’s MetaboLights; a source in the Omics Archives connector in Claude Science.
Molecule-MCP
MCP server · chatmol · GA · verified: works · security: caution
MCP bundle letting Claude drive PyMOL and ChimeraX visualization and run GROMACS molecular dynamics simulations via natural language.
Molfeat (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill wrapping Molfeat — a unified API over 100+ molecular featurizers spanning classical fingerprints, descriptors, and pre-trained chemical foundation-model embeddings.
MyGene.info MCP (BioThings)
MCP server · longevity-genie · GA · verified: works · security: cleared
Gene annotation and ID conversion across species via MyGene.info/BioThings; the Genes & Ontologies connector in Claude Science.
NovoMCP
MCP server · Quant NexusAI · Preview · verified: degraded · security: unknown
Hosted computational-chemistry engine MCP — ADMET, GFN2-xTB QM, GPU GROMACS MD, and AutoDock-GPU docking over a precomputed compound layer.
Ontology Lookup Service (OLS) MCP Server
MCP server · seandavi · Beta · verified: works · security: caution
Search and resolve terms across hundreds of biomedical ontologies via EMBL-EBI’s OLS; part of the Genes & Ontologies connector in Claude Science.
Paper Lookup (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles.
Proto-OKN MCP Server
MCP server · SBL-SDSC (San Diego Supercomputer Center) · Beta · verified: works · security: cleared
Natural-language access to 30+ NSF Proto-OKN scientific knowledge graphs (SPOKE biomedicine, BioBricks chemical safety, more) via SPARQL, schema inspection, and cross-graph bridging.
PubChem MCP Server
MCP server · JackKuo666 · GA · verified: works · security: caution
MCP server that lets Claude query PubChem for compounds by name, SMILES, CID, or formula and pull structure files.
PyTDC (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill driving PyTDC for Therapeutics Data Commons benchmarks — ADMET, drug-target / drug-drug interactions, drug response, molecular generation, retrosynthesis.
RDKit Agent
MCP server · scottmreed · Alpha · verified: works · security: caution
WASM-based cheminformatics CLI, Node library, and MCP server that validates, converts, and analyzes SMILES/SMIRKS/InChI with no Python runtime.
RDKit Cheminformatics Skill
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill providing RDKit recipes for SMILES parsing, descriptors, fingerprints, substructure search, reactions, and 2D/3D molecular generation.
RDKit MCP Server
MCP server · TandemAI · GA · verified: works · security: cleared
MCP server exposing the full RDKit API as discrete tool calls so Claude can run cheminformatics without executing Python locally.
Revvity Signals AI Connector
Claude.ai Connector · Revvity Signals Software · GA · verified: degraded · security: cleared
Claude.ai connector giving natural-language access to the Revvity Signals electronic lab notebook and connected R&D data.
Rhea (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Expert-curated biochemical reactions from Rhea (SIB); a source in the Chemistry connector in Claude Science.
Rowan
Claude Skill, MCP server · K-Dense / Rowan · GA · verified: works · security: caution
Cloud-native molecular modeling and medicinal-chemistry workflow platform, installable as a Claude Skill or an MCP server.
SAR Analysis (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Structure-activity relationship (SAR) analysis guide for drug discovery including molecular descriptor analysis, scaffold analysis, and activity cliff detection
Scholar Gateway Connector (Wiley)
MCP server · Wiley · Beta · verified: works · security: cleared
Wiley remote connector for peer-reviewed scholarly content — 3M+ articles, 300+ Life Sciences journals.
Scientific Brainstorming (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Creative research ideation and exploration.
Scientific Critical Thinking (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Evaluate scientific claims and evidence quality.
Small Molecule Discovery (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill for compound identification, analog search, bioactivity, ADMET, target prediction, and commercial sourcing across PubChem, ChEMBL, BindingDB, and vendor catalogs.
Synapse.org Connector
MCP server · Sage Bionetworks · GA · verified: works · security: cleared
Discovery and metadata retrieval across Synapse-hosted biomedical datasets and consortium projects.
ToolUniverse
MCP server · Zitnik Lab (Harvard Medical School) · MIT Lincoln Laboratory · GA · verified: works · security: cleared
Harvard / MIT MCP server bundling 600+ vetted scientific tools — literature, chemistry, omics, clinical trials — for AI-scientist-style hypothesis exploration.
TorchDrug (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
PyTorch-native graph neural networks for molecules and proteins.
UniChem (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API.
XTB MCP Server
MCP server · PhelanShao (community) · Beta
MCP server that builds, validates, and explains xtb semi-empirical quantum-chemistry input decks for optimizations, frequencies, MD, and spectroscopy.
ZINC (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query ZINC15/ZINC22 virtual compound libraries (1.4B compounds, 750M purchasable).
arXiv MCP Server
MCP server · blazickjp · GA · verified: works · security: cleared
Search and retrieve arXiv preprints (incl. q-bio) and metadata; part of the Literature Graph connector in Claude Science.
bio-research (Claude Code Plugin)
Claude Code Plugin · Anthropic · GA · verified: degraded · security: cleared
Umbrella plugin bundling 5 analysis skills and ~10 MCP connectors (PubMed, BioRender, ChEMBL, Synapse, Wiley, Open Targets, Benchling, etc.) for preclinical R&D.
instrument-data-to-allotrope
Claude Skill · Anthropic · GA · verified: works · security: cleared
Converts 40+ lab-instrument output formats to Allotrope Simple Model JSON / CSV for LIMS and data-lake ingestion.
matchms (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Spectral similarity and compound identification for metabolomics.
scientific-problem-selection
Claude Skill · Anthropic · GA · verified: works · security: caution
Structured framework for research project ideation, risk assessment, and troubleshooting, based on Fischbach & Walsh (Cell 2024).
smina (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Smina molecular docking CLI.
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