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| 1 | # AlphaFold Implementation Mindmap |
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| 2 | |||
| 3 | ## Implementation Status Overview |
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| 4 | - [x] Basic Setup Complete (Repository & Structure) |
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| 5 | - [x] Data Pipeline Ready (Data Available) |
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| 6 | - [ ] Model Running |
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| 7 | - [ ] Results Validation |
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| 8 | |||
| 9 | ## Data Pipeline |
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| 10 | - Input Processing |
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| 11 | - [x] FASTA sequence parsing (code available) |
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| 12 | - [x] MSA generation (code available) |
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| 13 | - [x] Template search (code available) |
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| 14 | - [x] Feature generation (code available) |
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| 15 | |||
| 16 | ## Model Architecture |
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| 17 | - Evoformer |
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| 18 | - [x] MSA stack (code available) |
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| 19 | - [x] Pair stack (code available) |
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| 20 | - [x] Attention mechanisms (code available) |
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| 21 | - Structure Module |
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| 22 | - [x] 3D coordinate prediction (code available) |
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| 23 | - [x] Confidence scoring (pLDDT) (code available) |
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| 24 | - [x] Recycling (code available) |
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| 25 | |||
| 26 | ## Dependencies |
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| 27 | - [ ] JAX |
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| 28 | - [ ] HH-suite |
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| 29 | - [ ] OpenMM |
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| 30 | - [ ] Kalign |
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| 31 | |||
| 32 | ## Execution Flow |
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| 33 | 1. [ ] Sequence Input |
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| 34 | 2. [ ] MSA Generation |
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| 35 | - [ ] Sequence search against databases |
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| 36 | - [ ] Multiple sequence alignment |
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| 37 | 3. [ ] Template Search |
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| 38 | 4. [ ] Feature Processing |
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| 39 | 5. [ ] Model Prediction |
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| 40 | 6. [ ] Structure Refinement |
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| 41 | 7. [ ] Output Generation |
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| 42 | |||
| 43 | ## Data Requirements |
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| 44 | - Location: /net/scratch2/caom/alphafold_data (✓ FOUND) |
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| 45 | - [x] BFD (small_bfd available) |
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| 46 | - [x] MGnify |
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| 47 | - [x] PDB70 |
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| 48 | - [x] UniRef90 |
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| 49 | - [x] UniProt |
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| 50 | - [x] PDB structure files (pdb_mmcif) |
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| 51 | - [x] Model parameters (params) |
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| 52 | - [x] Additional: uniref30, pdb_seqres |
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| 53 | |||
| 54 | ## Output Processing |
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| 55 | - [ ] PDB file generation |
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| 56 | - [ ] Confidence score visualization |
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| 57 | - [ ] Structure visualization |
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| 58 | - [ ] PyMOL integration |
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| 59 | - [ ] ChimeraX support |