"claude" matching MCP servers:

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

Enables LLM agents to search EMDB cryo-EM maps, look up UniProt proteins, compute ESM-2 sequence embeddings, retrieve cryo-EM maps from a protein sequence via a two-tower model, and search GEO DNA-methylation arrays, all through typed tools with structured output. Ships with a 40-question evaluation harness that runs Claude as the MCP client.

An MCP server that gives Claude access to NCBI Datasets v2 — search genome assembly metadata, retrieve taxonomy records, and download data packages without leaving your conversation.

Enables citation-grounded biomedical literature review by searching PubMed, retrieving abstracts from Europe PMC, and looking up gene and protein records from NCBI Gene and UniProt, with every cited PMID verified to exist and support its claim. All tools are read-only, so Claude can only cite papers actually retrieved and read during the session.

Enables Claude Desktop to read and drive analyses on the active MilliMap session, including datasets, clusters, annotations, and markers.

Enables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.

Run real bioinformatics from your AI agent on your own GPUs: MMseqs2 homology search, ESMFold structure prediction and sequence tools for Claude, Cursor and Codex. GPU-aware scheduling for shared machines, fail-fast input checks, background jobs, agent-friendly results and provenance for every run.

Integrates the miEAA 3.x bioinformatics platform with Claude Desktop, enabling microRNA enrichment analysis, identifier conversion between miRBase versions, and miRNA-precursor transformations through natural language.

Exposes a bio-hybrid neuromorphic simulation pipeline (SNN, consciousness proxies, FinalSpark NeuroPlatform) as MCP tools, resources, and prompts for AI assistants like Claude, Cursor, and VS Code.

Enables Claude, Cursor, or any MCP client to query public Drosophila connectome datasets and run in-silico experiments on them locally, with every answer carrying built-in controls, uncertainty, and provenance. Currently exposes dataset listing with licence, citation, download size, and locally cached level details.

Connects PyMOL to Claude AI through the Model Context Protocol, allowing for conversational structural biology and molecular visualization through natural language commands.

Lets Claude and ChatGPT open and drive a Spacewalk 3D chromatin viewer alongside the conversation.

Enables Claude and other MCP clients to run fast, exactly scored similarity and substructure searches over a local PubChem fingerprint index, pull live PubChem records (identifiers, synonyms, GHS, bioassays) with cited sources, and compute offline RDKit descriptors, med-chem alerts and highlighted structure drawings — all without API rate limits.

Enables AI assistants to query VCF files through MCP tools that summarize variants, identify pathogenic and carrier variants, interpret pharmacogenomic results, and determine APOE status, with web app and Claude Desktop support.

BioOpenMCP enables users to run bioinformatics tools like FastQC, Cutadapt, and STAR with background execution and status checking. It integrates with Claude Desktop to perform quality control, trimming, alignment, and reporting via natural language.

Enables Claude Code to interact with a TACC or SLURM HPC cluster for bioinformatics pipelines, allowing job management, log reading, file browsing, remote script execution, and job submission through natural language.

Manages local protein experiments with a Flask backend and SQLite, offering tools for protein library management, Beer-Lambert concentration calculations, BLI dilution planning, and experiment archiving. It provides 7 MCP tools for AI assistants like Claude to interact with the system.