AlterLab AlphaFold (via ColabFold)
Kører AlphaFold2 via ColabFold for at folde proteiner/komplekser og fortolke pLDDT/pTM/ipTM/PAE-konfidens.
Virker med opsætning
Hvad det gør
Forudsiger 3D protein structures from a FASTA sequence using AlphaFold2 through ColabFold's MMseqs2-accelerated MSA pipeline, covering single-chain monomers and AlphaFold2-Multimer complexes. Forklarer how to read per-residue and per-interface confidence metrics and how to validate a designed sequence via self-consistency refolding. Part of a larger AlterLab suite; explicitly defers to sibling skills for ligand co-folding, antibody complexes, embeddings, or database lookups. Kræver a CUDA GPU and ColabFold install.
Testrapport
Dirigerer Correctly a ProteinMPNN-designed peptide into the self-consistency fold-and-check loop and hands the GPU step off to alterlab-remote-compute -- but actual folding needs a CUDA GPU plus multi-GB AlphaFold2 weights that this sandbox doesn't have, so only the guidance layer could be verified.
Testet: 2026-07-14 · Claude Code 2.x (agent harness)
Installation
git clone https://github.com/AlterLab-IEU/AlterLab-Academic-Skills cd AlterLab-Academic-Skills mkdir -p ~/.claude/skills cp -r skills/bioinformatics/alterlab-alphafold ~/.claude/skills/alterlab-alphafold
Kommandoer og eksempelprompter
/alterlab-alphafoldKører AlphaFold2 via ColabFold for at folde proteiner/komplekser og fortolke pLDDT/pTM/ipTM/PAE-konfidens.
Skills udløses af almindelige forespørgsler — ingen kommandoer at huske. Efter installationen aktiverer prompter som disse skillen (på engelsk):
Fold this FASTA sequence and give me pLDDT confidence scores.Predict this protein complex structure with AlphaFold2-Multimer.I designed this peptide with ProteinMPNN, check if it folds back.