# EBI Proteins MCP for AI Agents AI Agent Connect > EBI Proteins API MCP. Access the UniProt knowledge base to pull protein sequences, functional annotations, and genetic variant data directly into your AI client. It connects your agent to millions of entries for molecular biology research, clinical genomics, and proteomics analysis without manual database navigation. ## Overview - **Category:** the-unthinkable - **Price:** Free - **Endpoint:** https://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/ai-agent-connect - **Tags:** proteins, uniprot, bioinformatics, genomics, variants, proteomics, embl-ebi ## Description Imagine you're deep in a research project and need to know every documented variant for a specific protein. Instead of opening a new tab, hunting through the UniProt database, and copy-pasting data into a spreadsheet, you just ask your agent to do it. This Connector puts the entire EMBL-EBI Proteins API at your fingertips. It lets you pull everything from basic sequence features like binding sites and signal peptides to complex proteomics data like mass-spectrometry peptide evidence. You can map proteins to genome coordinates or dig into curated mutagenesis experiments to see how specific mutations affect protein function. It's like having a research assistant who already knows the entire UniProt knowledge base by heart. By using this Connector through the Vinkius catalog, you turn your AI client into a specialized bioinformatics tool that handles the heavy lifting of data retrieval so you can focus on the actual science. ## Tools ### get_proteomics Access mass-spectrometry proteomics data for a protein. This lets you see which peptides were experimentally detected and if they're unique. ### get_antigen Retrieve peptide regions used for antibody generation. This is useful for identifying validated expression targets in immunology research. ### get_coordinates Map a protein to genome coordinates on GRCh38 or GRCh37. This bridges protein annotations with Ensembl gene and transcript IDs. ### get_protein_features Get sequence annotations including domains, active sites, and disulfide bonds. Use this to see the physical features of a protein's structure. ### get_genecentric Get the gene-centric view of a proteome including canonical protein counts. Use this to see how many proteins relate to each gene in a specific proteome. ### get_mutagenesis Retrieve mutagenesis experiments and their phenotypic effects. This helps you understand how specific mutations impact protein structure and function. ### get_protein Fetch a complete protein entry using a UniProt accession. Use this to get names, sequences, and cross-references in one go. ### get_proteome Get details for a specific proteome, including taxonomy and protein counts. Use this to identify the components of a specific organism's proteome. ### get_proteomics_ptm Retrieve residue-level post-translational modification positions. Use this to see evidence counts from mass-spec data. ### get_taxonomy Get scientific names, ranks, and lineage for a specific NCBI taxon ID. Use this to navigate the tree of life for a specific organism. ### get_variation Fetch genetic variants from sources like ClinVar and gnomAD. This provides clinical significance and consequence types for protein mutations. ### search_features_by_type Search for specific features like domains, binding sites, or signal peptides across proteins. Use this to find specific structural motifs quickly. ### search_proteins Search for proteins using gene names, organisms, or keywords. This returns a summary list of matching proteins and their sequence lengths. ### search_proteomes Search for proteomes by organism name like "homo sapiens". This helps you find the correct proteome ID for a specific species. ### search_taxonomy Find taxonomy entries by organism name to get the correct taxon ID. Use this as a first step before querying specific proteins or proteomes. ### search_variation Search for clinically relevant variants by consequence type or source. Use this to find specific types of mutations across the proteome. ## Prompt Examples **Prompt:** ``` What are the known binding sites for the human insulin receptor? ``` **Response:** ``` I've checked the features for the human insulin receptor (INSR). Here are the key binding sites: | Feature Type | Start | End | Evidence Count | | --- | --- | --- | --- | | BINDING | 124 | 140 | 12 | | BINDING | 450 | 468 | 8 | It also has several transmembrane regions and signal peptides. ``` **Prompt:** ``` Give me the genome coordinates for the BRCA1 protein on GRCh38. ``` **Response:** ``` The BRCA1 protein (P38398) maps to the following coordinates on the GRCh38 assembly: * **Chromosome:** 17 * **Ensembl Gene ID:** ENSG00000012048 * **Transcript ID:** ENST00000357654 * **Strand:** - (Reverse) This mapping allows you to cross-reference protein-level variant annotations with specific genomic positions. ``` **Prompt:** ``` Are there any known mutagenesis experiments for the TP53 protein? ``` **Response:** ``` Yes, there are several documented mutagenesis experiments for TP53. * **Mutation:** R175H * **Effect:** Loss of DNA binding activity * **Mutation:** Y220C * **Effect:** Increased protein stability These experiments show how different mutations impact the protein's functional state and help guide experimental design. ``` ## Capabilities ### Pull full protein entries Fetch complete records including names, sequences, and cross-references by UniProt accession. ### Extract sequence features Get specific data on binding sites, domains, signal peptides, and disulfide bonds. ### Fetch genetic variants Access aggregated variant data from sources like ClinVar, gnomAD, and COSMIC. ### Query proteomics data Retrieve mass-spectrometry peptide evidence and post-translational modification positions. ### Map to genome coordinates Link proteins to specific chromosome positions and Ensembl IDs on GRCh38 or GRCh37. ### Navigate biological taxonomy Search and retrieve lineage, ranks, and scientific names for any organism. ## Use Cases ### Variant Analysis A clinical geneticist asks for all known mutations of a specific tumor suppressor protein. The agent uses get_variation to pull clinical significance and population frequencies from gnomAD and ClinVar. ### Structural Mapping A structural biologist needs to find all binding sites for a specific enzyme. The agent uses get_protein_features to list every binding site and its specific location on the sequence. ### Genomic Alignment A bioinformatician needs to map a protein to its specific chromosome position. The agent uses get_coordinates to return the Ensembl gene ID and exact start/end positions on GRCh38. ### Proteome Survey A researcher wants to see the protein count and taxonomy for a specific organism. The agent uses search_proteomes and get_proteome to provide a full overview of the species' proteome. ## Benefits - Stop manually searching UniProt. Use get_protein to pull complete entries with sequences and cross-references in one step. - Speed up clinical assessments. Use get_variation to pull aggregated data from ClinVar and gnomAD instantly. - Simplify structural analysis. Use get_protein_features to identify binding sites and domains without browsing complex web pages. - Automate genomic mapping. Use get_coordinates to link proteins to Ensembl gene and transcript IDs on GRCh38. - Access deep proteomics data. Use get_proteomics and get_proteomics_ptm to see experimental evidence for peptide detection and modifications. - Navigate biological taxonomy easily. Use search_taxonomy and get_taxonomy to find the correct IDs for any organism quickly. ## How It Works The bottom line is you get instant, programmatic access to the world's largest protein database without needing an API key. 1. Subscribe to the EBI Proteins API MCP on Vinkius. 2. Connect the Connector to your preferred client like Claude, Cursor, or Windsurf. 3. Ask your agent to fetch protein sequences, variants, or coordinates. ## Frequently Asked Questions **Can I use the EBI Proteins API MCP to get protein sequences?** Yes, you can use this Connector to pull full protein sequences, names, and cross-references for any UniProt accession. It's a fast way to get the raw data you need for your research. **Does the EBI Proteins API MCP require an API key?** No, the EBI Proteins API is fully public, so you don't need to worry about managing keys or subscriptions. You can start querying data as soon as you connect it. **Can I find clinical variants like those from ClinVar using this?** Yes, this Connector pulls aggregated genetic variant data from sources like ClinVar and gnomAD. It's great for seeing clinical significance and consequence types for mutations. **Does this Connector support genome mapping?** Yes, it can map proteins to specific coordinates on the GRCh38 and GRCh37 assemblies. It provides Ensembl gene and transcript IDs to help link proteins to genomic data. **Can I use the EBI Proteins API MCP for proteomics research?** Absolutely. You can query mass-spectrometry proteomics data, including peptide evidence and post-translational modifications (PTMs). **How do I find the correct taxonomy ID for a specific organism?** You can use the search tools within the Connector to find the correct NCBI taxon ID by organism name. This ensures you're querying the right data for your species. **Do I need an API key to use this server?** No. The EMBL-EBI Proteins API is completely public and requires no authentication. Simply subscribe to this server and enter any placeholder value in the API key field to start querying protein data immediately. **What kind of variant data is available?** The server aggregates genetic variants from multiple authoritative sources: UniProtKB curated variants, ClinVar clinical significance data, gnomAD population frequencies, 1000 Genomes Project, COSMIC somatic mutations, TOPMed whole-genome sequencing, ExAC exome data, and TCGA cancer variants. Each variant includes consequence type, clinical significance, and source cross-references. **Can I map protein positions to genome coordinates?** Yes. The get_coordinates tool maps any UniProt protein to reference genome coordinates on GRCh38 and GRCh37 assemblies. It returns Ensembl gene, transcript, and translation identifiers along with chromosome, start/end positions, and strand orientation. This bridges the gap between protein-level annotations and genomic-level analyses.