alphagem

name	alphagem
description	AlphaGEM — genome-scale metabolic modelling aided by protein structure alignment and deep-learning dark-metabolism mining. Use when: (1) Building or refining GEMs beyond sequence-only gap filling, (2) Integrating structure signals into metabolic networks, (3) Comparing to gapseq / VMH workflows. Upstream: https://github.com/hongzhonglu/AlphaGEM. Route via metagenomics-llm; pair with gapseq / vmh for classical GEM context.
license	MIT
category	analysis-tools
tags	["AlphaGEM","GEM","metabolism","structure","deep-learning"]
upstream	https://github.com/hongzhonglu/AlphaGEM
stage	mining

AlphaGEM

Upstream: hongzhonglu/AlphaGEM

Citation

Han, W. et al. AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining. Nat. Commun. (2026). https://doi.org/10.1038/s41467-026-75549-w

See also docs/references.md.

Analytical thinking

Sequence-only GEM reconstruction misses “dark” metabolism. AlphaGEM combines structure alignment with DL mining to improve genome-scale models. Use on high-quality genomes/MAGs after mag-qc; interpret human/gut context with vmh when relevant.

Models remain computational — not measured fluxes. Pin AlphaGEM version, structure sources (e.g. AFDB), and gap-filling rules.

How to run

# follow upstream README for structure DBs and GEM reconstruction steps

Decision tree

Metabolic modelling need?
├─ Classical pathway/GEM from MAG → gapseq
├─ Structure + dark metabolism mining → alphagem
├─ Human/gut knowledge integration → vmh
└─ Annotation distillate only → dram

Related skills

metagenomics-llm · gapseq · vmh · dram · deepblast · mag-qc · microbial-mining · tool-selection