Drug Repurposing and Discovery

Installable Claude components for target identification, virtual screening, lead optimization, ADMET prediction, drug-repurposing knowledge graphs, and end-to-end discovery agents.

10x Genomics Cloud MCP

MCP server · 10x Genomics · GA

Conversational orchestration of 10x Cloud single-cell, immune-profiling, and spatial-transcriptomics analyses.

K-Dense skill that submits designed protein and antibody sequences to the Adaptyv cloud lab for wet-lab binding, expression, thermostability, and activity assays, with NetSolP/SoluProt/SolubleMPNN/ESM/ipTM/pSAE pre-screening.

AdisInsight Plugin

Claude Code Plugin · Springer Nature · GA

Springer Nature AdisInsight MCP plugin surfacing drug-development pipeline, clinical-trial, and deal intelligence to Claude for repurposing and competitive scouting.

AlphaFold MCP Server

MCP server · Augmented Nature · GA

MCP server exposing the EBI AlphaFold Protein Structure Database for structure retrieval, pLDDT analysis, comparison, and PyMOL/ChimeraX export.

Anthropic PubMed Connector

MCP server · Anthropic · GA

Anthropic-managed NCBI literature search via PubMed and PubMed Central.

Arboreto (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for gene-regulatory-network inference with Arboreto — GRNBoost2 / GENIE3 tree-based regression over bulk or single-cell expression, distributed via Dask.

AutoDock Vina (Claude Skill)

Claude Skill · SciAgent · GA

Molecular docking with AutoDock Vina (Python API).

BGPT Paper Search (Claude Skill)

Claude Skill · K-Dense · GA

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.

BioContextAI Knowledgebase MCP

MCP server · BioContextAI · GA

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

Unified biomedical lookup across PubMed, ClinicalTrials.gov, MyVariant, and OpenFDA.

BioPython (Claude Skill)

Claude Skill · K-Dense · GA

Comprehensive molecular biology toolkit.

BioRender Connector

MCP server · BioRender · GA

Scientific-figure assembly from the 50,000+ BioRender icon and template library.

BioServices (Claude Skill)

Claude Skill · K-Dense · GA

Unified Python interface to 40+ bioinformatics services.

Biomni (Claude Skill)

Claude Skill · Stanford SNAP Lab · GA

General-purpose biomedical AI agent that plans and runs multi-step research workflows across genomics, drug discovery, and clinical analysis.

COBRApy (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill driving COBRApy for constraint-based metabolic modelling — FBA, FVA, gene knockouts, flux sampling, gapfilling on SBML genome-scale models.

ChEMBL Connector

Claude Code Plugin · EMBL-EBI (Anthropic-packaged) · GA

Anthropic-packaged plugin and Claude.ai connector over EMBL-EBI’s ChEMBL bioactive-compound database — compound, target, bioactivity, and mechanism-of-action lookup.

ChemLint

MCP server · molML (TU/e) · GA

MCP server exposing 150+ molecular machine-learning tools — SMILES cleaning, descriptors, similarity, clustering, model training — so Claude runs cheminformatics ML without Python scripting.

ClinPGx (PharmGKB) (Claude Skill)

Claude Skill · SciAgent · GA

Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations …

ClinicalTrials.gov MCP Server (cyanheads)

MCP server · cyanheads (Casey Hand) · GA

Apache-2.0 MCP server over the ClinicalTrials.gov v2 API — trial search, full study records, outcomes / adverse-event extraction, and patient-to-trial matching. Hosted public instance available.

Composer

Plugin · Scripps AI Enablement · Beta

Turns a plain-language scientific problem into a grounded, runnable Claude solution composed from this catalog, reusing recipes and recommending autonomous systems.

Consensus Plugin

Claude Code Plugin · Consensus · GA

Consensus.app MCP plugin bringing AI-powered scientific literature search and evidence synthesis into Claude across all research areas.

Cortellis Plugin

Claude Code Plugin · Clarivate · GA

Clarivate Cortellis MCP plugin surfacing global drug-pipeline, clinical-trial, regulatory, safety, and deals intelligence to Claude for competitive scouting and regulatory work.

CovaSyn Chemistry MCP

MCP server · CovaSyn · GA

Hosted deterministic cheminformatics MCP with 130+ tools spanning ADMET, docking, retrosynthesis, ICH M7 toxicology, NMR/MS, and biologics design.

DDInter (Claude Skill)

Claude Skill · SciAgent · GA

Query DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs).

DailyMed (Claude Skill)

Claude Skill · SciAgent · GA

Query FDA drug labels (DailyMed) via REST API.

Database Lookup (Claude Skill)

Claude Skill · K-Dense · GA

Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs.

Datamol (Claude Skill)

Claude Skill · K-Dense · GA

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

Claude skill driving DeepChem for molecular machine learning — graph neural nets (GCN, GAT, MPNN, AttentiveFP), featurization, and the MoleculeNet benchmarks (toxicity, ADMET, quantum properties).

DepMap (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for querying the Cancer Dependency Map — CRISPR Chronos gene-effect scores, PRISM drug sensitivity, mutation, expression, and CN data across cancer cell lines.

DiffDock (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill driving DiffDock, a diffusion-based deep-learning docker that predicts protein–ligand binding poses from PDB plus SMILES with per-pose confidence scores.

Drug Repurposing (Claude Skill)

Claude Skill · Zitnik Lab (Harvard Medical School) · GA

ToolUniverse agent skill that finds drug-repurposing candidates via target-, compound-, and disease-driven strategies with mechanism and feasibility scoring.

DrugBank MCP Server

MCP server · openpharma-org (community) · GA

Community MCP server exposing a local DrugBank SQLite (17k+ drugs) with 16 query methods for repurposing, target lookup, interactions, and structural similarity.

Ensembl MCP Server

MCP server · effieklimi · GA

MCP server over the Ensembl REST API for gene/transcript lookup, sequence retrieval, variant consequences, comparative genomics, and assembly lift-over.

Glycoengineering (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for protein-glycosylation analysis — N-glycosylation sequon scanning, O-glycosylation hotspot prediction, and access to NetOGlyc/GlycoShield/GlycoWorkbench for therapeutic antibody and vaccine design.

Guide to Pharmacology (GtoPdb) (Claude Skill)

Claude Skill · SciAgent · GA

Query IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and approved drugs.

Hypothesis Generation (Claude Skill)

Claude Skill · K-Dense · GA

Structured hypothesis formulation from observations.

Literature Review (Claude Skill)

Claude Skill · K-Dense · GA

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).

MedChem (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill wrapping MedChem — drug-likeness filters (Lipinski, Veber, Egan, Muegge), ADMET-flag detection, and medicinal-chemistry alerts on top of RDKit.

Molecular Dynamics (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill that runs and analyzes OpenMM molecular dynamics simulations and MDAnalysis trajectory analyses for proteins, ligands, and biomolecular complexes.

Molecule-MCP

MCP server · chatmol · GA

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

Claude skill wrapping Molfeat — a unified API over 100+ molecular featurizers spanning classical fingerprints, descriptors, and pre-trained chemical foundation-model embeddings.

Open Targets (Claude Skill)

Claude Skill · SciAgent · GA

Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety.

Open Targets Plugin

Claude Code Plugin · Open Targets · GA

Official Open Targets MCP plugin giving Claude GraphQL access to target-disease associations, drug evidence, and target-prioritisation scores.

OpenFDA MCP Server (ythalorossy)

MCP server · Ythalo Saldanha · GA

MIT-licensed npm MCP server over the openFDA drug API — adverse events, safety/labeling, manufacturer lookups, and NDC resolution.

Owkin Pathology Explorer Connector

Claude.ai Connector · Owkin · GA

Owkin’s Pathology Explorer agent — H&E whole-slide image analysis, cell-type detection, and tumour-microenvironment profiling — exposed to Claude as a remote MCP connector.

PDB MCP Server

MCP server · Augmented Nature · GA

MCP server that lets Claude search, fetch, and validate RCSB Protein Data Bank structures with PDBe/UniProt cross-referencing.

Paper Lookup (Claude Skill)

Claude Skill · K-Dense · GA

Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles.

PrimeKG (Claude Skill)

Claude Skill · K-Dense · GA

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

PubChem MCP Server

MCP server · JackKuo666 · GA

MCP server that lets Claude query PubChem for compounds by name, SMILES, CID, or formula and pull structure files.

PyDESeq2 (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for bulk RNA-seq differential expression with PyDESeq2 — size factors, dispersion, Wald / LRT testing, BH-adjusted p-values.

PyTDC (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill driving PyTDC for Therapeutics Data Commons benchmarks — ADMET, drug-target / drug-drug interactions, drug response, molecular generation, retrosynthesis.

RDKit MCP Server

MCP server · TandemAI · GA

MCP server exposing the full RDKit API as discrete tool calls so Claude can run cheminformatics without executing Python locally.

Rowan

Claude Skill, MCP server · K-Dense / Rowan · GA

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

Structure-activity relationship (SAR) analysis guide for drug discovery including molecular descriptor analysis, scaffold analysis, and activity cliff detection

Scanpy-MCP

MCP server · scmcphub · GA

MCP server wrapping Scanpy so Claude can run end-to-end single-cell RNA-seq analyses (QC, clustering, DE, plotting) from natural language.

Scholar Gateway Connector (Wiley)

MCP server · Wiley · Beta

Wiley remote connector for peer-reviewed scholarly content — 3M+ articles, 300+ Life Sciences journals.

Scientific Brainstorming (Claude Skill)

Claude Skill · K-Dense · GA

Creative research ideation and exploration.

Scientific Critical Thinking (Claude Skill)

Claude Skill · K-Dense · GA

Evaluate scientific claims and evidence quality.

Synapse.org Connector

MCP server · Sage Bionetworks · GA

Discovery and metadata retrieval across Synapse-hosted biomedical datasets and consortium projects.

ToolUniverse

MCP server · Zitnik Lab (Harvard Medical School) · MIT Lincoln Laboratory · GA

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

PyTorch-native graph neural networks for molecules and proteins.

UniChem (Claude Skill)

Claude Skill · SciAgent · GA

Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API.

UniProt MCP Server

MCP server · Augmented Nature · GA

MCP server giving Claude 26 tools over the UniProt REST API for protein search, domains, orthologs, PTMs, pathways, and multi-format export.

ZINC (Claude Skill)

Claude Skill · SciAgent · GA

Query ZINC15/ZINC22 virtual compound libraries (1.4B compounds, 750M purchasable).

bio-research (Claude Code Plugin)

Claude Code Plugin · Anthropic · GA

Umbrella plugin bundling 5 analysis skills and ~10 MCP connectors (PubMed, BioRender, ChEMBL, Synapse, Wiley, Open Targets, Benchling, etc.) for preclinical R&D.

clinical-trial-protocol (Anthropic Healthcare Plugin)

Claude Code Plugin · Anthropic · GA

Anthropic Claude Code plugin that drafts FDA/NIH-compliant Phase 2/3 clinical-trial protocols for drugs or devices via a waypoint-based workflow.

gget (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill wrapping the gget command-line / Python tool for fast unified queries against Ensembl, UniProt, NCBI, PDB, COSMIC, and other genomics databases.

instrument-data-to-allotrope

Claude Skill · Anthropic · GA

Converts 40+ lab-instrument output formats to Allotrope Simple Model JSON / CSV for LIMS and data-lake ingestion.

nextflow-development

Claude Skill · Anthropic · GA

Runs nf-core rnaseq, sarek, and atacseq pipelines on local FASTQ or GEO/SRA inputs.

openFDA (Claude Skill)

Claude Skill · SciAgent · GA

Query openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement.

scientific-problem-selection

Claude Skill · Anthropic · GA

Structured framework for research project ideation, risk assessment, and troubleshooting, based on Fischbach & Walsh (Cell 2024).

scvi-tools

Claude Skill · Anthropic · GA

Deep-learning workflows for scVI, scANVI, totalVI, MultiVI, PeakVI, DestVI, and related scvi-tools models for single-cell omics.

single-cell-rna-qc

Claude Skill · Anthropic · GA

scverse MAD-based QC for .h5ad and 10x .h5 single-cell RNA-seq inputs.

smina (Claude Skill)

Claude Skill · SciAgent · GA

Smina molecular docking CLI.

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