AlphaFold Implementation Mindmap

Implementation Status Overview

• Basic Setup Complete (Repository & Structure)
• Data Pipeline Ready (Data Available)
• Model Running
• Results Validation

Data Pipeline

• Input Processing
• FASTA sequence parsing (code available)
• MSA generation (code available)
• Template search (code available)
• Feature generation (code available)

Model Architecture

• Evoformer
• MSA stack (code available)
• Pair stack (code available)
• Attention mechanisms (code available)
• Structure Module
• 3D coordinate prediction (code available)
• Confidence scoring (pLDDT) (code available)
• Recycling (code available)

Dependencies

• JAX
• HH-suite
• OpenMM
• Kalign

Execution Flow

1. Sequence Input
2. MSA Generation
3. Sequence search against databases
4. Multiple sequence alignment
5. Template Search
6. Feature Processing
7. Model Prediction
8. Structure Refinement
9. Output Generation

Data Requirements

• Location: /net/scratch2/caom/alphafold_data (✓ FOUND)
• BFD (small_bfd available)
• MGnify
• PDB70
• UniRef90
• UniProt
• PDB structure files (pdb_mmcif)
• Model parameters (params)
• Additional: uniref30, pdb_seqres

Output Processing

• PDB file generation
• Confidence score visualization
• Structure visualization
• PyMOL integration
• ChimeraX support