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 · verified: degraded · security: caution
Conversational orchestration of 10x Cloud single-cell, immune-profiling, and spatial-transcriptomics analyses.
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.
Adaptyv (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
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.
Alignment Trimming (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Trim multiple sequence alignments with ClipKIT, trimAl, BMGE, Divvier or HMMcleaner, choosing the mode by downstream goal rather than by habit
AlphaFold MCP Server
MCP server · Augmented Nature · GA · verified: works · security: caution
MCP server exposing the EBI AlphaFold Protein Structure Database for structure retrieval, pLDDT analysis, comparison, and PyMOL/ChimeraX export.
AlphaFold2 (Claude Skill)
Claude Skill · Google DeepMind · GA · verified: works · security: cleared
AlphaFold2 protein/complex structure prediction, run locally or via a hosted API with an optional ColabFold MSA server; a Claude Science skill.
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.
Binding Site Detection (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Find and rank druggable pockets on an apo protein with fpocket, P2Rank, CASTp and DoGSiteScorer — including cryptic pockets over an MD ensemble
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.
Blatant-Why (BY) Protein Design Agent
Claude Code Plugin · 001TMF · Beta · verified: works · security: caution
Scaffolds a Claude Code antibody and nanobody design campaign — 19 skills, 13 slash commands, and 11 MCP servers wired to design models and cloud compute.
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.
Chai-1 (Claude Skill)
Claude Skill · Chai Discovery · GA · verified: works · security: cleared
Chai-1 biomolecular structure prediction (proteins, nucleic acids, ligands) run locally or via a hosted server; a Claude Science skill.
ChimeraX MCP Server
MCP server · mahynotch · GA · verified: works · security: caution
Drive UCSF ChimeraX from Claude in natural language — open, mutate, visualize, measure, and render protein structures; ChimeraX auto-launches.
Complex Portal (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Curated macromolecular complexes from EMBL-EBI’s Complex Portal; a source in the Structures & Interactions connector in Claude Science.
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.
Covariation Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Test whether a proposed RNA secondary structure is actually supported by evolutionary covariation, using R-scape and an explicit statistical-power check
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.
DiffDock (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
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.
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.
EMDB (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
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 · verified: works · security: cleared
Comprehensive toolkit for EvolutionaryScale protein language models including ESM3 (generative multimodal design across sequence, structure, and function) and ESM C (efficient embeddings).
ESMFold (Claude Skill)
Claude Skill · Meta AI / EvolutionaryScale · GA · verified: works · security: caution
ESMFold single-sequence protein structure prediction (no MSA), run locally or via the ESM Atlas API; a Claude Science skill.
Ensembl MCP Server
MCP server · effieklimi · GA · verified: works · security: cleared
MCP server over the Ensembl REST API for gene/transcript lookup, sequence retrieval, variant consequences, comparative genomics, and assembly lift-over.
Foldseek Structural Search (Claude Skill)
Claude Skill · Google DeepMind · GA · verified: degraded · security: cleared
Submit a 3D protein structure (.pdb/.cif) and find structurally similar proteins across AFDB, PDB100, SwissProt, and more via the Foldseek API.
GPCR Structural Pharmacology (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA
ToolUniverse agent skill for GPCR drug discovery — ligand classification, GPCRdb structures, mutation effects, and antibody-antigen interface analysis.
GROMACS MCP Server
MCP server · MacromNex · Alpha · verified: works · security: caution
Run GROMACS molecular-dynamics simulations and trajectory analysis from Claude via a Docker container with GROMACS 2025.4 pre-installed.
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.
Geometric Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Measure static protein structures with Bio.PDB — distances, dihedrals, superposition and RMSD, radius of gyration, and SASA — with the caveats stated
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.
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.
IntAct (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Molecular-interaction evidence from EMBL-EBI’s IntAct database; a source in the Structures & Interactions connector in Claude Science.
InterPro (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query InterPro REST API for protein domain architecture, family classification, and member-DB integration.
Interface Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Map protein-protein and protein-ligand interfaces with Bio.PDB — contact residues, buried surface area, and telling a real interface from crystal packing
LigandMPNN (Claude Skill)
Claude Skill · Baker Lab, UW Institute for Protein Design · GA · verified: works · security: cleared
LigandMPNN ligand-aware protein sequence design (fixed-backbone) accounting for small molecules, metals, and nucleotides; a Claude Science skill.
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.).
MDAnalysis (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS.
MDTraj (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Mdtraj molecular dynamics trajectory analysis (Python).
MSA Statistics (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Compute percent identity, conservation scores, gap profiles and substitution-matrix statistics over a multiple alignment with BioPython, and read them correctly
Molecular Dynamics (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
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 · verified: works · security: caution
MCP bundle letting Claude drive PyMOL and ChimeraX visualization and run GROMACS molecular dynamics simulations via natural language.
Multiple Sequence Alignment (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Build multiple sequence alignments with MAFFT, MUSCLE5, Clustal Omega or T-Coffee, choosing the algorithm by dataset size and divergence
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.
OpenFold3 (Claude Skill)
Claude Skill · OpenFold Consortium / AQ Laboratory · GA · verified: works · security: cleared
OpenFold3 open-source biomolecular structure prediction (AlphaFold-class), run locally; a Claude Science skill.
OpenMM MCP Server
MCP server · PhelanShao (community OSS) · GA · verified: works · security: caution
MCP server that sets up and runs OpenMM molecular dynamics simulations (protein, membrane, advanced sampling) and Abacus DFT jobs from natural language.
PDB MCP Server
MCP server · RCSB PDB · GA · verified: works · security: cleared
MCP servers that let Claude search, fetch, and validate RCSB Protein Data Bank structures — including the official first-party RCSB server.
PDBe MCP Servers
MCP server · PDBe (EMBL-EBI) · GA · verified: works · security: cleared
First-party PDBe Europe MCP servers giving Claude access to protein structure data via REST API, Solr search, and an optional Neo4j graph.
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.
Protein MCP Server
MCP server · cyanheads · GA · verified: works · security: cleared
Federated protein-structure search across experimental (PDB) and predicted (AlphaFold) models — homolog search, structural alignment, ligand and annotation lookup, keyless.
ProteinMPNN (Claude Skill)
Claude Skill · Baker Lab, UW Institute for Protein Design · GA · verified: works · security: cleared
ProteinMPNN deep-learning fixed-backbone protein sequence design; runs locally as a Claude Science skill.
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.
PyMOL (Claude Skill)
Claude Skill · Google DeepMind · GA · verified: degraded · security: cleared
Visualize, align, and render protein/molecular structures with PyMOL — headless, GPU-free, producing publication-quality PNGs and editable .pse sessions.
RNA Structure Probing (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Turn SHAPE-MaP or DMS-MaPseq reads into per-nucleotide reactivity profiles with ShapeMapper2, then fold RNA with those reactivities as soft restraints
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.
Rosetta MCP Server
MCP server · Ariel Ben-Sasson (community OSS) · GA · verified: works · security: caution
MCP server for Rosetta, PyRosetta and Biotite — run and validate RosettaScripts, score structures, translate protocols between the three APIs
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.
STRING (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species).
Scanpy-MCP
MCP server · scmcphub · GA · verified: works · security: caution
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 · 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.
Seqera MCP
MCP server · Seqera Labs · GA · verified: works · security: cleared
Hosted MCP server for launching and managing Nextflow/nf-core pipelines on the Seqera Platform and retrieving public SRA/ENA/GEO sequencing data.
SolubleMPNN (Claude Skill)
Claude Skill · Baker Lab, UW Institute for Protein Design · GA · verified: works · security: cleared
Soluble-optimized ProteinMPNN weights that bias sequence design away from exposed hydrophobics; a Claude Science skill.
Structural Alignment (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Superpose and score protein structures with Foldseek, TM-align, US-align, DALI or FoldMason when sequence identity is too low to align reliably
Structure Preparation (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Make a deposited or predicted structure docking- or MD-ready with PDBFixer, reduce, PROPKA and PDB2PQR — hydrogens, tautomers, missing atoms, short loops
Structure Validation (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Decide whether a structure or region is reliable enough to build on — resolution, R-free gap, B-factors, MolProbity geometry, and pLDDT/PAE for predicted models
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.
UniProt MCP Server
MCP server · Augmented Nature · GA · verified: works · security: caution
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 · verified: works · security: cleared
Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings.
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.
gget (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill wrapping the gget command-line / Python tool for fast unified queries against Ensembl, UniProt, NCBI, PDB, COSMIC, and other genomics databases.
ncRNA Search (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Find non-coding RNA homologs and assign Rfam families with Infernal covariance models, scoring sequence and secondary structure together
nextflow-development
Claude Skill · Anthropic · GA · verified: works · security: cleared
Runs nf-core rnaseq, sarek, and atacseq pipelines on local FASTQ or GEO/SRA inputs.
pyOpenMS (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Complete mass spectrometry analysis platform.
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).
scvi-tools
Claude Skill · Anthropic · GA · verified: works · security: cleared
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 · verified: works · security: cleared
scverse MAD-based QC for .h5ad and 10x .h5 single-cell RNA-seq inputs.
smina (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Smina molecular docking CLI.
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