"An Introduction to the Python Programming Language" matching MCP servers:

An MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.

Enables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.

Provides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.

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

Enables AI agents to search, filter, download files, and generate reports from the IGVF Data Portal using natural language commands.

Enables AI agents to control RELION 5.x cryo-EM structure determination software through natural language, providing 23 tools for the complete single-particle analysis pipeline.

An MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.

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

An MCP server for the gget bioinformatics library that enables AI assistants to perform complex genomics queries, including gene sequence retrieval, BLAST alignments, and protein structure predictions.

Enables AI agents to query the WikiPathways open community pathway database via natural language, part of the Pipeworx MCP gateway.

An MCP server that enables language models to fetch protein information from the UniProt database, including protein details, sequences, functions, and structures.

Control PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.

An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

MCP server that provides tools to query harmonized gene-disease validity data from the Gene Curation Coalition, supporting consensus and conflict detection for gene-disease assertions.

Enables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).

Enables DNA sequence analysis and variant effect prediction using Evo2-7B via MCP tools, providing forward inference, likelihood scoring, and batch variant comparison through natural language.

Enables coding agents to interact with the Reactome pathway database, including search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set enrichment analysis.