"Resources or Assistance for Learning to Code" matching MCP servers:

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.

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.

A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.

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 quantum machine learning operations using Qiskit, including executing quantum circuits, computing quantum kernels, training variational quantum classifiers, and evaluating quantum ML models.

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 RNA structure analysis, sequence evaluation, and inverse design using geometric deep learning models. Supports both quick computational analysis and long-running batch processing for generating RNA sequences that fold into target structures.

Enables protein stability prediction ($DeltaDelta$G and $Delta$Tm) and systematic mutation analysis using the SPIRED-Stab deep learning model. It supports single variant analysis, batch processing, and job monitoring via Docker-based inference.

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.

Enables prediction of blood-brain barrier permeability for drug molecules via machine learning, with molecule name lookup, plain-language explanations, similar drug search, and applicability domain checks. Exposes these as MCP tools and orchestrates them via a LangGraph agent.

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.

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.

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.

A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.

A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.

Enables agents to search a public PubMed-derived corpus by natural language or identifiers and to retrieve publication details while traversing bounded citation and semantic literature graphs.

Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.

A stateless, deterministic Bio-Robotics Core Engine converting biological data (UniProt API) to G-code.

Enables interaction with MGnify metagenomics resources and tools through the Model Context Protocol. Provides access to MGnify's API for querying and analyzing metagenomic datasets and related biological information.