Phase 1A biological review

Operational viability

8 / 8
All targets are acceptable for the bounded local-runtime claim.

Biological generality

blocked
The set is mixed and caveated, not biologically representative.

Needs review

human
External biological review is still pending before biological generality claims.

Decision

The Phase 1A set is suitable for a first-paper operational viability claim: SimpleFold-3B ran and scored across a frozen mixed-context set on an M3 Max workstation. It is not suitable for broad biological generality claims. The target mix is useful precisely because it includes clean X-ray cases, membrane/transport stress cases, long enzyme contexts, and complex-derived coverage probes.

Review Summary

Bucket	Count
Acceptable for operational viability	6
Acceptable with coverage caveat	1
Acceptable with context caveat	1
Blocked for biological generality	2

Target-Level Caveats

Target	Context class	Recommendation	Caveat
`13CZ:A`	paired membrane lipoprotein control	`acceptable`	Paired DcrB pH structures are useful controls but should not overweight one protein family in broader claims.
`13EE:A`	paired membrane lipoprotein control	`acceptable`	Paired DcrB pH structures are useful controls but should not overweight one protein family in broader claims.
`13FT:A`	clean lipid-transfer domain	`acceptable`	No major biological caveat beyond single-run computational-benchmark scope.
`11BC:C`	complex-derived coverage probe	`coverage caveat`	Only 63 aligned reference residues were scored, so lDDT supports operational/scoring QA but not a full-chain biological-quality claim.
`12OY:A`	membrane complex stress case	`context caveat`	Membrane/complex cryo-EM context and 3.6 A resolution make this a stress case; use for viability, not biological generality.
`9H8N:A`	long membrane transport stress case	`acceptable`	Long membrane transporter cryo-EM target; strong for memory/runtime stress, cautious for general quality interpretation.
`9K9X:A`	long enzyme context	`acceptable`	No major biological caveat beyond single-run computational-benchmark scope.
`9K9Y:A`	long enzyme ligand context	`acceptable`	Ligand-bound context is useful, but this benchmark does not evaluate ligand placement or affinity.

Reviewer Questions

Are the paired DcrB structures acceptable as controls, or do they overweight one family?
Should 11BC:C remain in aggregate quality tables, or only in scoring-QA discussion?
Is 12OY:A acceptable as a membrane/complex stress case despite 3.6 A resolution?
Can 9H8N:A be described as a transporter stress target without implying transporter-general performance?
Should 9K9Y:A mention ligand context only as provenance, with no ligand-quality interpretation?

Artifacts

Source document: docs/36_phase1a_biological_review.md. External biological review is still pending before biological generality claims.