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name: protein-workflows description: "Plan TorchDrug protein sequence, structure, contact prediction, function/property, ESM, GearNet, and protein-protein interaction workflows." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

Protein Workflows

Use this sub-skill when a user needs TorchDrug/TorchProtein guidance for protein data, residue or atom views, sequence/structure encoders, contact prediction, protein function/property prediction, ESM embeddings, or protein-protein interaction tasks.

Read First

• For protein object creation, dataset families, feature choices, representation model selection, graph construction, and ESM caveats, read references/protein-data-and-models.md.
• For end-to-end contact, protein property/function, and interaction/PPI affinity recipes, read references/task-workflows.md.
• For failures around downloads, sequence/PDB parsing, feature dimensions, truncation, ESM caches, memory, and contact labels, read references/troubleshooting.md.
• For an offline planning checklist, run python scripts/plan_protein_workflow.py --workflow contact, property, or interaction from this sub-skill directory.

Use This For

• Creating data.Protein / data.PackedProtein from sequences or PDB-derived structures.
• Choosing between ProteinCNN, ProteinResNet, ProteinLSTM, ProteinBERT, GearNet, ESM, and Physicochemical protein encoders.
• Planning ProteinNet contact prediction with tasks.ContactPrediction and residue coordinates/masks.
• Planning protein property, function, localization, stability, fluorescence, beta-lactamase, enzyme commission, or AlphaFoldDB workflows.
• Planning HumanPPI, YeastPPI, or PPIAffinity workflows with tasks.InteractionPrediction.

Route Elsewhere

• Use ../graph-data/SKILL.md for generic graph packing, masking, dataset containers, collators, and raw Graph mechanics.
• Use ../layers-and-extensions/SKILL.md for custom graph construction layers, new edge functions, compiled extension issues, or deep layer internals.
• Use ../training-engine/SKILL.md for core.Engine, optimizer/scheduler wiring, checkpoint save/load, config round-trips, logging, CPU/GPU selection, and distributed training.
• Use ../molecular-workflows/SKILL.md for small-molecule, reaction, generation, retrosynthesis, or ligand-property workflows.
• Use ../knowledge-graphs/SKILL.md for entity/relation triple reasoning and knowledge graph completion.