Extending ProteinTTT to protein pairs for complex structure prediction. We adapt masked-language-model
test-time training to jointly refine ESM2 representations of two interacting proteins, improving
DockQ scores for predicted protein-protein complex structures.
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All Experiments
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Method Overview
ProteinTTT-PPI Pipeline
Input: Protein A (sequence) + Protein B (sequence)
|
v
+------------------+ +-------------------+
| Concatenation | | Linker Strategy |
| A + [linker] + B | <-- | poly-G / flexible |
+------------------+ +-------------------+
|
v
+----------------------------+
| ESM-2 (650M) Embedding |
| Token representations |
+----------------------------+
|
v
+----------------------------+
| Test-Time Training (TTT) |
| Masked LM self-supervision |
| on the input pair |
+----------------------------+
|
v
+----------------------------+
| ESMFold Structure Module |
| Predict paired structure |
+----------------------------+
|
v
+----------------------------+
| DockQ Evaluation |
| Compare to native complex |
+----------------------------+
Masking Strategies
Random Uniform
M_KL_AGGGR_DE_K
15% random masking across both chains uniformly
Interface-Biased
MKL___GGG___EKR
Higher masking rate at predicted interface residues
Chain-Alternating
______GGGRDEKAL
Mask one full chain, predict from the other
Span Masking
M___ALGGGRD___K
Contiguous spans of 3-7 residues masked
Key Hyperparameters
| Parameter |
Value |
Description |
| model | ESM-2 (650M) | Base protein language model |
| ttt_steps | 100 | TTT gradient steps per sample |
| ttt_lr | 1e-5 | Learning rate for TTT updates |
| mask_ratio | 0.15 | Fraction of tokens masked |
| linker | poly-G (25) | Linker sequence between chains |
| max_length | 800 | Max total sequence length (A+linker+B) |
| num_recycles | 4 | ESMFold recycling iterations |
| batch_size | 1 | Per-sample TTT (no batching) |
Experiment Logs
[2026-03-25 12:00:00] INFO ProteinTTT-PPI initialized
[2026-03-25 12:00:00] INFO Awaiting experiment logs...
[2026-03-25 12:00:00] INFO Logs will auto-refresh every 5 minutes