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Found 77 Skills
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 up to 4000 sequences and a maximum file size of 4 MB. Do not use to search for homologous proteins in a database (use MMseqs2, BLAST), align non-protein sequences (DNA, RNA), perform structural alignment (use Foldseek, PyMOL), or if you only have a single sequence.
Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.
Expert in Galaxy workflow development, testing, and IWC best practices. Create, validate, and optimize .ga workflows following Intergalactic Workflow Commission standards.
Query the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices (PWMs) for specific TFs, resolving gene symbols to JASPAR Matrix IDs, or getting TF metadata. Supports multiple output formats (MEME, TRANSFAC, PFM, JASPAR, YAML).
Query the QuickGO and Evidence & Conclusion Ontology (ECO) REST API. Use this when you need to map genes to biological processes, molecular functions, or cellular components, find genes associated with a specific pathway/GO term, or explore the Gene Ontology hierarchy. Do not use for querying drug targets (use OpenTargets) or mechanistic signaling pathway diagrams (use KEGG).
Prioritize drug targets from a ranked gene list (e.g., scRNA-seq DE output) by orchestrating parallel API queries against UniProt, OpenTargets (with integrated DepMap CRISPR essentiality + gnomAD constraint), PubMed, the Human Protein Atlas (HPA), and ChEMBL tool compounds, then re-ranking by a composite score combining protein localization, druggability, disease genetics, tissue specificity (safety), focus-cell-type expression, CRISPR essentiality, LoF safety constraint, and research maturity. Use whenever the user wants to filter, triage, prioritize, or "do due diligence" on a list of candidate genes for drug discovery, especially after a DE / DEG analysis when they say things like "which of these should I follow up on", "filter for druggable targets", "make a target dossier", "rank these for tractability", "annotate these genes for druggability", or "build a target report". Trigger even when the user says just "filter these candidate genes" or hands over a CSV from a DE pipeline.
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
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. InterPro combines 14 databases (e.g., Pfam, CDD) into one searchable resource. InterPro-N significantly expands annotation and sequence coverage with deep learning. Includes domain architecture (IDA) search.
Integrate structural biology data with proteomics for drug target validation. Retrieves protein structures from PDB (RCSB, PDBe), AlphaFold predictions, antibody structures (SAbDab), GPCR data (GPCRdb), binding pocket analysis (ProteinsPlus), and ligand interactions (BindingDB). Use when asked to find structures for a drug target, identify binding site ligands, cross-validate drug binding with structural data, assess structural druggability, or compare experimental vs predicted structures.
OpenBio API for biological data access and computational biology tools. Use when: (1) Querying biological databases (PDB, UniProt, ChEMBL, etc.), (2) Searching scientific literature (PubMed, bioRxiv, arXiv), (3) Running structure prediction (Boltz, Chai, ProteinMPNN), (4) Performing pathway/enrichment analysis, (5) Designing molecular biology experiments (primers, cloning), (6) Analyzing variants and clinical data.
Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or analyze protein-ligand interactions. Do not use for docking, molecular dynamics, or sequence-only analysis.