Research & Analysis Workflows

Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome plot. Use Prokka for legacy pipelines or non-bacterial kingdoms; PGAP for NCBI GenBank submission.

mdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories; computes RMSD vs time, radius of gyration, per-residue RMSF, residue-residue contact frequency maps, phi/psi torsions for Ramachandran plots (general + Gly/Pro), and 8-state DSSP secondary structure. Modules: trajectory I/O, geometry (distances/angles/dihedrals), structural analysis (RMSD/Rg/RMSF/SASA), contacts, hydrogen bonds, secondary structure (DSSP), NMR observables. For broader atom-selection grammar use mdanalysis-trajectory; for running MD simulations use OpenMM/GROMACS.

Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. Parse molecules and reactions from .cdxml/.cdx, write structures with good 2D depiction, and hand-build or modify the parts RDKit cannot write: reaction arrows, plus signs, schemes/steps, and text/labels. Use for reaction schemes, synthesis routes, mechanisms, retrosynthesis, or SI figures. Critical: RDKit writes structures only — round-tripping a reaction through a Mol silently drops arrows and text; this skill shows the XML layer that preserves them. For pure molecular analysis (descriptors, fingerprints, SMARTS) use rdkit-cheminformatics; for multi-format 3D conversion use openbabel.

Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with -e), and a pan-genome reference. Use Panaroo for higher-accuracy pan-genomes from highly fragmented assemblies, PIRATE for paralog-aware clustering, or PPanGGOLiN for graph-based partitioning.

Scaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name}/SKILL.md with valid frontmatter, appends the registry.yaml entry, runs validation. Enforces name uniqueness, kebab-case, description keyword rules, schema rules from CLAUDE.md.

smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns. Pipeline: receptor PDBQT prep -> ligand prep (RDKit/OpenBabel) -> dock via autobox or explicit grid -> rescore/minimize with custom scoring -> rank poses by affinity. Choose smina over Vina when you need custom scoring terms (--customscoring), local optimization of an existing pose (--localonly), per-atom contributions (--atomtermdata), or SDF/MOL2 ligands without manual PDBQT conversion. For unknown binding sites use diffdock; for the Python-bindings/Vinardo workflow use autodock-vina-docking.