Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Schema
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_proteins | Search UniProt database for proteins by name, keyword, or organism |
| get_protein_info | Get detailed information for a specific protein by UniProt accession |
| search_by_gene | Search for proteins by gene name or symbol |
| get_protein_sequence | Get the amino acid sequence for a protein |
| get_protein_features | Get functional features and domains for a protein |
| compare_proteins | Compare multiple proteins side-by-side with sequence and feature comparison |
| get_protein_homologs | Find homologous proteins across different species |
| get_protein_orthologs | Identify orthologous proteins for evolutionary studies |
| get_phylogenetic_info | Retrieve evolutionary relationships and phylogenetic data |
| get_protein_structure | Retrieve 3D structure information from PDB references |
| get_protein_domains_detailed | Enhanced domain analysis with InterPro, Pfam, and SMART annotations |
| get_protein_variants | Disease-associated variants and mutations |
| analyze_sequence_composition | Amino acid composition, hydrophobicity, and other sequence properties |
| get_protein_pathways | Associated biological pathways (KEGG, Reactome) |
| get_protein_interactions | Protein-protein interaction networks |
| search_by_function | Search proteins by GO terms or functional annotations |
| search_by_localization | Find proteins by subcellular localization |
| batch_protein_lookup | Process multiple accessions efficiently |
| advanced_search | Complex queries with multiple filters (length, mass, organism, function) |
| search_by_taxonomy | Search by detailed taxonomic classification |
| get_external_references | Links to other databases (PDB, EMBL, RefSeq, etc.) |
| get_literature_references | Associated publications and citations |
| get_annotation_confidence | Quality scores for different annotations |
| export_protein_data | Export data in specialized formats (GFF, GenBank, etc.) |
| validate_accession | Check if accession numbers are valid |
| get_taxonomy_info | Detailed taxonomic information for organisms |