"Resources for Coding in Python" matching MCP servers:

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.

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 resolve scientific names to Taxonomic Serial Numbers, traverse complete taxonomic lineages from kingdom to children, and retrieve vernacular names in all languages from an authoritative US-government taxonomy.

Enables querying gene expression experiments, brain region structure ontologies, and in-situ hybridization datasets from the Allen Institute's Brain Atlas public API.

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

Executes SPARQL queries against biological and biomedical RDF databases from the RDF Portal, with additional REST API integrations for bioinformatics resources.

A unified MCP server for biomedical research that connects AI systems to resources like Ensembl, EuropePMC, STRING, and more, enabling retrieval of verified domain-specific information.

Enables in-chat scientific viewers for molecular structures, sequence alignments, and slide images, plus data tools for searching structures, fetching sequences, aligning them, and drafting NGS analysis plans.

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

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.

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.

MCP server exposing REINVENT4 generative molecular-design operations as validated, LLM-callable tools for drug discovery, including sampling, transfer learning, reinforcement learning, and molecular analysis.

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

A Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.

Provides read-only access to the ProPaths verified protein interactome, letting AI agents search proteins, retrieve mechanistic interaction details, and explore pathway ontology through MCP tools, resources, and prompts.

Renders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.

Empowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.

An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.