eigen-reprod-atlas — paper drafts

Apple Silicon viability of AF3-class protein structure prediction: a single-researcher agentic benchmark.
Authors: Raúl Chío León¹·², Yocanxóchitl Perfecto-Avalos², Luis Eduardo Falcón-Morales²
¹ Eigen Biotech (umbrella) · ² Tecnológico de Monterrey, Campus Guadalajara, Mexico

Status — 2026-05-11: Phase 0 POC complete. Pipeline reproduces 3/3 PDB targets with SimpleFold-100M on M3 Max via MLX. Draft updates as Phase 1 runs progress.

Phase 0 results (3 PDB targets, SimpleFold-100M, MLX on M3 Max)

Target	aa	lDDT	TM-score	RMSD	Wall (s)
1L2Y Trp-cage	20	0.969	0.680	0.38 Å	109
1CRN crambin	46	0.993	0.967	0.39 Å	774*
1UBQ ubiquitin	76	0.965	0.963	0.77 Å	110
Median		0.969	0.963	0.39 Å	110

* 774 s on 1CRN = first run including weight + ESM-2 download; warm runs ~110 s.

v1 Workshop paper draft

Full IMRaD draft (~1700 words). Sections 4 Results still has Phase 0 placeholders pending fill from atlas.json above.

Target venues: NeurIPS ML4H 2026 · ICLR ML4Science 2027 · bioRxiv preprint

Abstract draft

~260 word abstract. Numerical placeholders [X out of 5], [0.XX], [N], [Y] will fill from Phase 1 main runs.

Repository

github.com/Theovia/eigen-reprod-atlas (private during build phase)

Phase 0 findings doc, full architecture, MCP server source, M3 Max bridge, agent prompts.

Last updated: 2026-05-11 · Auto-refresh on repo push