Skill UI

Query InterPro for protein family, domain, and GO annotations via a REST API with Python helpers, enabling function prediction, domain architecture mapping, and evolutionary classification insights for proteomic workflows.

Run OpenMM-powered molecular dynamics simulations and MDAnalysis trajectory workflows to build protein or small-molecule systems, minimize energy, equilibrate conditions, and characterize RMSD/RMSF, contacts, and free-energy surfaces for structural biology or drug studies.

A comprehensive toolkit for reconstructing and analyzing the evolutionary history of biological sequences (genes, proteins, genomes). The standard workflow includes multiple sequence alignment using MAFFT, robust maximum likelihood tree inference with IQ-TREE 2 and FastTree, and advanced visualization/manipulation using ETE3. This skill is essential for studies in viral phylodynamics, microbial genomics, protein family evolution, and molecular clock dating.

Provides direct REST access to UniProt for searching proteins, retrieving sequences/annotations, mapping IDs, and streaming large datasets in workflows that demand precise protein data.