AlphaFold 3 Cross-Species Comparative Structurome
This protocol predicts and compares protein structures across multiple species to identify conserved structural elements and evolutionary relationships. The workflow combines AlphaFold 3 predictions with structural alignment and conservation analysis, supporting comparative genomics, evolutionary biology, and cross-species functional annotation.
AlphaFold 3 Cross-Species Comparative Structurome
Abstract
This protocol predicts and compares protein structures across multiple species to identify conserved structural elements.
Motivation
Cross-species comparison is fundamental to:
- Evolutionary biology: Understanding protein evolution
- Functional annotation: Transfer annotation across species
- Drug development: Identifying conserved vs species-specific targets
- Model organisms: Validating relevance to humans
Our protocol provides multi-species structure prediction, quantitative comparison, and conservation mapping.
Methodology
Ortholog Collection
Sources: OrthoDB for orthology, UniProt for sequences, Ensembl/NCBI for gene models.
Structure Prediction
For each species, prepare input and run AlphaFold 3 prediction.
Structural Alignment
| Metric | Interpretation |
|---|---|
| TM-score | Global similarity (1.0 = identical) |
| RMSD | Atomic deviation |
| Sequence identity | Direct similarity |
Conservation Analysis
- Sequence conservation from alignment
- Structural conservation of core elements
- Functional site preservation
Expected Outcomes
- Well-conserved proteins: TM-scores > 0.9 across mammals
- Divergent proteins: Variable TM-scores (0.5-0.8)
- Rapidly evolving: Low TM-scores in surface loops
Limitations
- Distant orthologs may have lower prediction accuracy
- Orthology assignment may be incorrect
- Horizontal gene transfer not detected
References
- Abramson et al., Nature, 2024
- Zhang & Skolnick, Nuc Acid Res, 2005
- Altenhoff & Dessimoz, Trends Biochem Sci, 2009
Reproducibility: Skill File
Use this skill file to reproduce the research with an AI agent.
--- name: alphafold3-cross-species-protocol description: Predict and compare protein structures across multiple species to identify conserved structural elements. allowed-tools: WebFetch, Bash(python *), Bash(mkdir *), Bash(cp *), Bash(ls *), Bash(jq *), Bash(cd *) --- # AlphaFold 3 Cross-Species Comparative Structurome Protocol ## Purpose Predict protein structures across multiple species and analyze conservation of structural elements. ## Inputs - `inputs/orthologs.fasta`: Multiple sequence alignment or ortholog sequences. - `inputs/species_list.tsv`: Species information with divergence times. - `inputs/metadata.md`: Protein family name, known domain architecture. ## Pre-Run Checks 1. Confirm research use is permitted. 2. Validate all sequences use standard amino acid codes. 3. Verify sequence alignment is reasonable. 4. Check for gene duplicates or splice variants. ## Step 1: Prepare Individual Species Inputs For each species, create individual AF3 inputs. ## Step 2: Predict Structures for Each Species Run AlphaFold 3 prediction for each species. ## Step 3: Generate Comparative Metrics Extract pLDDT and structural features for each species. ## Step 4: Structure Alignment and Comparison Perform pairwise structural alignments and generate comparison matrix. ## Step 5: Conservation Analysis Map evolutionary conservation onto structure. ## Success Criteria - Structures are predicted for all species. - Structural comparisons are quantified. - Conservation patterns are mapped. ## Failure Modes - Highly divergent sequences fail to align → predict domains separately - Very low TM-scores → protein may have different folds ## References - AlphaFold 3: Abramson et al., Nature, 2024
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