Integrative Structural and Computational Biology
Installable Claude components for protein and complex structure prediction, molecular dynamics, integrative modelling, cryo-EM analysis, and computational biology workflows that span structure, sequence, and dynamics.
10x Genomics Cloud MCP
MCP server · 10x Genomics · GA
Conversational orchestration of 10x Cloud single-cell, immune-profiling, and spatial-transcriptomics analyses.
Adaptyv (Claude Skill)
Claude Skill · K-Dense · GA
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.
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.
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.
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.
Database Lookup (Claude Skill)
Claude Skill · K-Dense · GA
Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs.
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.
EMDB (Claude Skill)
Claude Skill · SciAgent · GA
Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS.
ESM (Claude Skill)
Claude Skill · K-Dense · GA
Comprehensive toolkit for EvolutionaryScale protein language models including ESM3 (generative multimodal design across sequence, structure, and function) and ESM C (efficient embeddings).
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.
Hypothesis Generation (Claude Skill)
Claude Skill · K-Dense · GA
Structured hypothesis formulation from observations.
InterPro (Claude Skill)
Claude Skill · SciAgent · GA
Query InterPro REST API for protein domain architecture, family classification, and member-DB integration.
Literature Review (Claude Skill)
Claude Skill · K-Dense · GA
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).
MDAnalysis (Claude Skill)
Claude Skill · SciAgent · GA
Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS.
MDTraj (Claude Skill)
Claude Skill · SciAgent · GA
Mdtraj molecular dynamics trajectory analysis (Python).
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.
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.
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.
STRING (Claude Skill)
Claude Skill · SciAgent · GA
Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species).
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.
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.
ViennaRNA (Claude Skill)
Claude Skill · SciAgent · GA
Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings.
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.
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.
nextflow-development
Claude Skill · Anthropic · GA
Runs nf-core rnaseq, sarek, and atacseq pipelines on local FASTQ or GEO/SRA inputs.
pyOpenMS (Claude Skill)
Claude Skill · K-Dense · GA
Complete mass spectrometry analysis platform.
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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