This index provides a comprehensive mapping of all 32 algorithms from the AlphaFold2 supplementary materials to their source code implementations and explanation notebooks.
- ✅ Complete (includes pseudocode image, source code reference, NumPy implementation, and test examples)
| # | Algorithm | Notebook | Source File | Status |
|---|---|---|---|---|
| 1 | MSA Block Deletion | algorithm-1-MSABlockDeletion.ipynb | model/tf/data_transforms.py |
✅ |
| 2 | Inference | algorithm-2-Inference.ipynb | model/modules.py:AlphaFold |
✅ |
| 3 | Input Embedder | algorithm-3-InputEmbedder.ipynb | model/modules.py:EmbeddingsAndEvoformer |
✅ |
| 4 | relpos | algorithm-4-relpos.ipynb | model/modules.py:EmbeddingsAndEvoformer |
✅ |
| 5 | one_hot | algorithm-5-one_hot.ipynb | jax.nn.one_hot |
✅ |
| 6 | Evoformer Stack | algorithm-6-EvoformerStack.ipynb | model/modules.py:EvoformerIteration |
✅ |
| 7 | MSA Row Attention with Pair Bias | algorithm-7-MSARowAttentionWithPairBias.ipynb | model/modules.py:MSARowAttentionWithPairBias |
✅ |
| 8 | MSA Column Attention | algorithm-8-MSAColumnAttention.ipynb | model/modules.py:MSAColumnAttention |
✅ |
| 9 | MSA Transition | algorithm-9-MSATransition.ipynb | model/modules.py:Transition |
✅ |
| 10 | Outer Product Mean | algorithm-10-OuterProductMean.ipynb | model/modules.py:OuterProductMean |
✅ |
| 11 | Triangle Multiplication (Outgoing) | algorithm-11-TriangleMultiplicationOutgoing.ipynb | model/modules.py:TriangleMultiplication |
✅ |
| 12 | Triangle Multiplication (Incoming) | algorithm-12-TriangleMultiplicationIncoming.ipynb | model/modules.py:TriangleMultiplication |
✅ |
| 13 | Triangle Attention (Starting Node) | algorithm-13-TriangleAttentionStartingNode.ipynb | model/modules.py:TriangleAttention |
✅ |
| 14 | Triangle Attention (Ending Node) | algorithm-14-TriangleAttentionEndingNode.ipynb | model/modules.py:TriangleAttention |
✅ |
| 15 | Pair Transition | algorithm-15-PairTransition.ipynb | model/modules.py:Transition |
✅ |
| 16 | Template Pair Stack | algorithm-16-TemplatePairStack.ipynb | model/modules.py:TemplatePairStack |
✅ |
| 17 | Template Pointwise Attention | algorithm-17-TemplatePointwiseAttention.ipynb | model/modules.py:Attention |
✅ |
| 18 | Extra MSA Stack | algorithm-18-ExtraMsaStack.ipynb | model/modules.py:ExtraMsaStack |
✅ |
| 19 | MSA Column Global Attention | algorithm-19-MSAColumnGlobalAttention.ipynb | model/modules.py:GlobalAttention |
✅ |
| 20 | Structure Module | algorithm-20-StructureModule.ipynb | model/folding.py:StructureModule |
✅ |
| 21 | Rigid from 3 Points | algorithm-21-rigidFrom3Points.ipynb | model/r3.py:rigids_from_3_points |
✅ |
| 22 | Invariant Point Attention | algorithm-22-InvariantPointAttention.ipynb | model/folding.py:InvariantPointAttention |
✅ |
| 23 | Backbone Update | algorithm-23-BackboneUpdate.ipynb | model/folding.py:FoldIteration |
✅ |
| 24 | Compute All Atom Coordinates | algorithm-24-computeAllAtomCoordinates.ipynb | model/all_atom.py |
✅ |
| 25 | makeRotX | algorithm-25-makeRotX.ipynb | model/all_atom.py |
✅ |
| 26 | Rename Symmetric Ground Truth Atoms | algorithm-26-renameSymmetricGroundTruthAtoms.ipynb | model/folding.py:compute_renamed_ground_truth |
✅ |
| 27 | Torsion Angle Loss | algorithm-27-torsionAngleLoss.ipynb | model/folding.py:supervised_chi_loss |
✅ |
| 28 | Compute FAPE | algorithm-28-computeFAPE.ipynb | model/all_atom.py:frame_aligned_point_error |
✅ |
| 29 | Predict Per-Residue LDDT | algorithm-29-predictPerResidueLDDT.ipynb | model/modules.py:PredictedLDDTHead |
✅ |
| 30 | Recycling (Inference) | algorithm-30-RecyclingInference.ipynb | model/modules.py:AlphaFold |
✅ |
| 31 | Recycling (Training) | algorithm-31-RecyclingTraining.ipynb | model/modules.py:AlphaFold |
✅ |
| 32 | Recycling Embedder | algorithm-32-RecyclingEmbedder.ipynb | model/modules.py:EmbeddingsAndEvoformer |
✅ |
- Algorithm 1: MSA Block Deletion
- Algorithm 3: Input Embedder
- Algorithm 4: relpos (Relative Position Encoding)
- Algorithm 5: one_hot
- Algorithm 6: Evoformer Stack
- Algorithm 7: MSA Row Attention with Pair Bias
- Algorithm 8: MSA Column Attention
- Algorithm 9: MSA Transition
- Algorithm 10: Outer Product Mean
- Algorithm 11-12: Triangle Multiplication (Outgoing/Incoming)
- Algorithm 13-14: Triangle Attention (Starting/Ending Node)
- Algorithm 15: Pair Transition
- Algorithm 16: Template Pair Stack
- Algorithm 17: Template Pointwise Attention
- Algorithm 18: Extra MSA Stack
- Algorithm 19: MSA Column Global Attention
- Algorithm 20: Structure Module
- Algorithm 21: Rigid from 3 Points
- Algorithm 22: Invariant Point Attention (IPA)
- Algorithm 23: Backbone Update
- Algorithm 24: Compute All Atom Coordinates
- Algorithm 25: makeRotX
- Algorithm 26: Rename Symmetric Ground Truth Atoms
- Algorithm 27: Torsion Angle Loss
- Algorithm 28: Compute FAPE
- Algorithm 29: Predict Per-Residue LDDT (pLDDT)
- Algorithm 30: Recycling (Inference)
- Algorithm 31: Recycling (Training)
- Algorithm 32: Recycling Embedder
- Algorithm 2: Inference