# Protein Pocket Design on CrossDocked and Binding MOAD

Source: [Protein Pocket Design on CrossDocked and Binding MOAD](<https://www.sota2.com/research/sota/protein-pocket-design-on-crossdocked-and-binding-moad>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2026-02-26T05:59:49.990Z

Evaluation of protein pocket design models using the CrossDocked and Binding MOAD dataset, focusing on structural accuracy metrics such as RMSD for bond lengths and dihedral angles.

A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage.

| Scope | Recorded value |
| --- | --- |
| Task | Protein Pocket Design |
| Dataset (including any stated split) | CrossDocked and Binding MOAD |
| Metric | RMSD (Bond lengths) |
| Unit | SCALAR |
| Direction | Lower is better |
| Results loaded | 6 of 6 |
| Coverage | All results currently returned for this benchmark |

Evaluation settings may differ between results. The original papers and recorded configurations are needed to establish comparability. A shared metric name alone does not establish an identical protocol.

## Metrics

- [RMSD (Bond lengths)](<https://www.sota2.com/research/sota/protein-pocket-design-on-crossdocked-and-binding-moad.md?metric=RMSD%20(Bond%20lengths)>): Lower is better; unit: SCALAR.

- [RMSD (Dihedral angles)](<https://www.sota2.com/research/sota/protein-pocket-design-on-crossdocked-and-binding-moad.md?metric=RMSD%20(Dihedral%20angles)>): Lower is better; unit: SCALAR.

## Recorded results

| Method | RMSD (Bond lengths) | Result date | Report paper |
| --- | --- | --- | --- |
| FAIR | 0.35 | Not recorded | 68fa5f511e209131ce9e8fe0 |
| MEAN | 0.44 | Not recorded | 68fa5f511e209131ce9e8fe0 |
| PocketOptimizer | 0.47 | Not recorded | 68fa5f511e209131ce9e8fe0 |
| Diffusion | 0.49 | Not recorded | 68fa5f511e209131ce9e8fe0 |
| DEPACT | 0.68 | Not recorded | 68fa5f511e209131ce9e8fe0 |
| HSRN | 0.76 | Not recorded | 68fa5f511e209131ce9e8fe0 |

### FAIR

RMSD (Bond lengths): 0.35. Result ID: 698bc2f97a967eddb7712cc3.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f511e209131ce9e8fe0.md>)

[Method origin paper](<https://www.sota2.com/research/paper/68fa5f511e209131ce9e8fe0.md>)

[Implementation](<https://github.com/zaixizhang/FAIR>)

Recorded evaluation configuration: Not recorded. This record does not assert independent reproduction.

### MEAN

RMSD (Bond lengths): 0.44. Result ID: 698bc2f97a967eddb7712cc2.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f511e209131ce9e8fe0.md>)

[Method origin paper](<https://www.sota2.com/research/paper/68fa5f481e209131ce9e8b6a.md>)

Recorded evaluation configuration: Not recorded. This record does not assert independent reproduction.

### PocketOptimizer

RMSD (Bond lengths): 0.47. Result ID: 698bc2f97a967eddb7712cbe.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f511e209131ce9e8fe0.md>)

Recorded evaluation configuration: Not recorded. This record does not assert independent reproduction.

### Diffusion

RMSD (Bond lengths): 0.49. Result ID: 698bc2f97a967eddb7712cc1.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f511e209131ce9e8fe0.md>)

Recorded evaluation configuration: Not recorded. This record does not assert independent reproduction.

### DEPACT

RMSD (Bond lengths): 0.68. Result ID: 698bc2f97a967eddb7712cbf.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f511e209131ce9e8fe0.md>)

Recorded evaluation configuration: Not recorded. This record does not assert independent reproduction.

### HSRN

RMSD (Bond lengths): 0.76. Result ID: 698bc2f97a967eddb7712cc0.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f511e209131ce9e8fe0.md>)

Recorded evaluation configuration: Not recorded. This record does not assert independent reproduction.

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