chai1-structure-prediction

name	chai1-structure-prediction
description	Run pinned Chai-1 inference for proteins, complexes, nucleic acids, ligands, covalent bonds, templates, or restraints. Use when multimolecular structure prediction needs Chai-1-specific inputs and confidence outputs.
license	MIT

Chai-1 Structure Prediction

Gate

Ask once before installing a pinned chai_lab release, downloading weights, using GPU compute, or contacting public MSA/template servers. Name each remote host and never upload private sequences or structures without approval. Follow $cx-compute-environment.

Workflow

1. Define every entity and state: protein/RNA/DNA sequence, ligand SMILES/CCD, modifications, stoichiometry, covalent bonds, restraints, and templates.
2. Pin Chai-1 version/commit, weight checksum, input schema, MSA/template mode, number of samples, seeds, hardware, precision, and all restraints.
3. Smoke-test chai-lab fold --help and an upstream example. Run the validated FASTA/context into artifacts/<run-id>/chai1/; preserve inputs, MSAs, templates, restraint files, structures, scores, logs, and failures.
4. Separate model confidence, interface confidence, geometry checks, and any downstream affinity estimate. Compare samples and inspect clashes, ligand state, covalent geometry, low-confidence regions, and restraint satisfaction.
5. Record with $science-provenance; use $science-review before conclusions.

Boundaries

• Restraint satisfaction is not independent evidence when restraints were input.
• A plausible complex or ligand pose is not proof of binding or affinity.
• Report results from public ColabFold-style MSAs separately from local MSAs.