research▌

### Protein Sequence Similarity Search - name: "protein-sequence-similarity-search" - description: "Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find ho..."

### Literature Search Biorxiv - name: "literature-search-biorxiv" - description: "Browse, filter, and download life sciences, biology, and medical preprints from bioRxiv and medRxiv. Supports fetching paper metadata by DOI, and browsing by date range with category and keyword filte..."

### Ensembl Database - name: "ensembl-database" - description: "Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP)...."

### Scienceskillscommon - name: "scienceskillscommon" - description: "Shared Python package for Science Skills, currently containing http_client -- a unified HTTP client with rate limiting, retries, and exponential backoff. Not a standalone agent skill. Do not invoke di..."

### Reactome Database - name: "reactome-database" - description: "Query the Reactome database (Analysis and Content Services). Use when the user asks about pathway analysis, gene list enrichment, retrieving results by token, finding unmapped or not-found identifiers..."

### Embl Ebi Ols - name: "embl-ebi-ols" - description: "Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (e.g., GO, DOID, HP). Use when the user asks to search fo..."

### Chembl Database - name: "chembl-database" - description: "Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechan..."

### Encode Ccres Database - name: "encode-ccres-database" - description: "Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when..."

### Interpro Database - name: "interpro-database" - description: "Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms. In..."

### Protein Sequence Msa - name: "protein-sequence-msa" - description: "Performs multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports ..."