Content
87%Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.
Tight, actionable content with executable commands and well-organized sections; the main gap is the absence of an explicit validation/verification step before passing batch-designed sequences to downstream folding, which is the one place a feedback loop would matter.
Suggestions
Add a 'Verify designs' step after the run (e.g. inspect score=/seq_recovery= values and confirm the fixed-residue positions were held) before the 'Next: fold ...' pointer, to give the batch workflow an explicit checkpoint.
Note that output FASTA contains the input sequence as the first record and that ProteinMPNN does not write designed-sequence PDBs, so the reader knows to expect sequences-only output before deciding to fold.
| Dimension | Reasoning | Score |
|---|---|---|
Conciseness | Lean and dense throughout — it skips explaining what proteins or inverse folding are and instead packs operational detail (flags, gotchas, checkpoint table, error table); the opening prose earns its place as decision guidance for choosing vs ligandmpnn/solublempnn rather than filler. | 3 / 3 |
Actionability | Provides a complete, copy-paste-ready bash block (pip install, git clone, full python invocation with flags) plus concrete error-recovery commands (e.g. `grep '^ATOM' file.pdb | cut -c22 | sort -u`) and exact output paths — fully executable, not pseudocode. | 3 / 3 |
Workflow Clarity | Steps are present (install → clone → run → inspect out/seqs) and there is a reactive error table, but for a batch operation (num_seq_per_target, temperature sweep) there is no explicit validate-the-output-before-proceeding checkpoint, which caps the score at 2 per the batch-operations guideline. | 2 / 3 |
Progressive Disclosure | A single self-contained file with well-organized sections (Running it, fixed_positions gotcha, Checkpoints, Errors) and no nested or deep references; no bundle files are needed, so clear sectioning alone satisfies the bar. | 3 / 3 |
Total | 11 / 12 Passed |