"Exploring a GitHub repository and creating a detailed flowchart of its functionality" matching MCP servers:

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 variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

Enables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.

Enables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

A production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.

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.

MCP server that exposes DECIMER image-to-SMILES functionality as tool calls.

A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.

Official public, read-only Helena Bioinformatics MCP for source-cited answers about the company and its published products.

Enables molecular generation, optimization, and analysis through NVIDIA MolMIM API. Supports generating drug-like molecules with desired properties, extracting molecular embeddings, and exploring chemical space around seed molecules.

A Model Context Protocol server that enables retrieval of -omics data from sources like PDB, ChEMBL, UniProt, PubChem, and HUGO.

MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.

MCP server that exposes STRING database functionality, allowing AI agents to resolve protein identifiers, retrieve interaction networks, perform homology lookups, and run functional enrichment analysis.

Annotate variants by with a deep and rich set of data. Can annotate: genetic change, rsID, CAid, HGVS (g./c./p.), protein change.

Enables AI assistants to create, monitor, and manage computational tasks through GA4GH Task Execution Service (TES) functionality. Provides seamless access to TES-compliant services for executing bioinformatics and scientific computing workflows.

A Model Context Protocol server providing programmatic access to 3D protein structural data from RCSB PDB, PDBe, and UniProt, enabling search, retrieval, comparison, and analysis of protein structures.

An MCP server that wraps R scripts for microbiome and amplicon (16S/ITS) analysis, providing tools for alpha/beta diversity, differential abundance, networks, and more, with PNG/PDF outputs.

A collaborative BrAPI v2.1 workspace for multi-agent research via MCP, enabling search and retrieval of studies, germplasm, genotypes, and more across any BrAPI v2-compliant server.

Resolves free-text condition and disease strings — trial-registry condition fields, drug-label indications, hand-typed wording — onto the Mondo Disease Ontology, returning the best term id and label along with a trustworthy match-quality label (exact label/synonym, broader, narrower, fuzzy, or no-match) plus cross-ontology xrefs. Optionally expands a resolved term to all of its descendant ids for building subtype-inclusive registry filters.