TAS-DB MCP Server
A Model Context Protocol server exposing ~7,000 predicted TCR-pMHC structures from the Jonsson Lab TAS-DB ImmRep subset to AI agents.
Endpoint
POST /api/mcpStreamable HTTP transport. Also accepts GET (SSE stream) and DELETE (session teardown).
Authentication
Authorization: Bearer <MCP_API_KEY>At this time, a private API key is required for access. If you are interested in using the MCP server, please contact the Jonsson Lab at UCSC to request credentials or inquire about public access plans.
Available Tools (8)
Structures
search_structures(antigen_symbol?, mhc_allele?, v_gene?, j_gene?, cdr3_pattern?, min_iptm?, organism?, category?, limit?, offset?)Search TCR-pMHC structures by antigen, MHC allele, V/J gene, CDR3 pattern, quality, or organism/category. Starting point for most queries.
get_structure_detail(structure_id)Full metadata for one structure: TCR gene alleles, CDR loop sequences, MHC alleles, antigen info, all AlphaFold confidence scores, experimental methods, and donor metadata.
Bonds
query_bonds(structure_id, bond_type?, chain_role?, pep_position?)PLIP-derived molecular bonds for a single structure with optional filters by bond type, chain role, or peptide position. Returns individual bond rows plus summary counts.
get_conserved_contacts(antigen_symbol, chain_role?, bond_type?, min_iptm?, min_structures?)Contacts conserved across multiple structures targeting the same antigen. Identifies binding motifs. Set min_structures higher for stricter conservation.
get_peptide_contact_map(antigen_symbol?, structure_id?, chain_role?, bond_type?, min_iptm?)Per-position peptide contact frequency broken down by chain role and bond type. Aggregates across an antigen or analyzes a single structure.
TCR Repertoire
search_by_tcr(trbv_gene, cdr3b, max_distance?, limit?)Find similar TCRs by TRBV gene prefix match, ranked by CDR3β Levenshtein distance. Use when given a TCR sequence to find similar structures.
get_gene_usage(antigen_symbol, chain?, gene_type?, min_iptm?)V/J gene usage frequencies for TCRs targeting an antigen. Filterable by alpha/beta chain and V/J type. Use for repertoire characterization.
Antigens
get_available_antigens(category?, organism?)List all antigens with peptides, TCR/structure counts, and mean ipTM, filterable by category or organism. Use as a discovery step.