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+# AlphaFold Implementation Mindmap
+
+## Implementation Status Overview
+- [x] Basic Setup Complete (Repository & Structure)
+- [x] Data Pipeline Ready (Data Available)
+- [ ] Model Running
+- [ ] Results Validation
+
+## Data Pipeline
+- Input Processing
+  - [x] FASTA sequence parsing (code available)
+  - [x] MSA generation (code available)
+  - [x] Template search (code available)
+  - [x] Feature generation (code available)
+
+## Model Architecture
+- Evoformer
+  - [x] MSA stack (code available)
+  - [x] Pair stack (code available)
+  - [x] Attention mechanisms (code available)
+- Structure Module
+  - [x] 3D coordinate prediction (code available)
+  - [x] Confidence scoring (pLDDT) (code available)
+- [x] Recycling (code available)
+
+## Dependencies
+- [ ] JAX
+- [ ] HH-suite
+- [ ] OpenMM
+- [ ] Kalign
+
+## Execution Flow
+1. [ ] Sequence Input
+2. [ ] MSA Generation
+   - [ ] Sequence search against databases
+   - [ ] Multiple sequence alignment
+3. [ ] Template Search
+4. [ ] Feature Processing
+5. [ ] Model Prediction
+6. [ ] Structure Refinement
+7. [ ] Output Generation
+
+## Data Requirements
+- Location: /net/scratch2/caom/alphafold_data (✓ FOUND)
+  - [x] BFD (small_bfd available)
+  - [x] MGnify
+  - [x] PDB70
+  - [x] UniRef90
+  - [x] UniProt
+  - [x] PDB structure files (pdb_mmcif)
+  - [x] Model parameters (params)
+  - [x] Additional: uniref30, pdb_seqres
+
+## Output Processing
+- [ ] PDB file generation
+- [ ] Confidence score visualization
+- [ ] Structure visualization
+  - [ ] PyMOL integration
+  - [ ] ChimeraX support