# Protein Pocket Generation on CrossDocked (test)

Source: [Protein Pocket Generation on CrossDocked (test)](<https://www.sota2.com/research/sota/protein-pocket-generation-on-crossdocked-test>)

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

Data updated: 2026-02-26T05:39:09.683Z

Evaluation of protein pocket generation models using the CrossDocked test set, focusing on specific interaction quality metrics such as Clash, Hydrogen Bonds (HB), Salt Bridges, Hydrophobic interactions, and Pi-Pi stacking.

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 Generation |
| Dataset (including any stated split) | CrossDocked (test) |
| Metric | Clash |
| 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

- [Clash](<https://www.sota2.com/research/sota/protein-pocket-generation-on-crossdocked-test.md?metric=Clash>): Lower is better; unit: SCALAR.

- [Hydrogen Bonds](<https://www.sota2.com/research/sota/protein-pocket-generation-on-crossdocked-test.md?metric=Hydrogen%20Bonds>): Higher is better; unit: SCALAR.

- [Salt Bridges](<https://www.sota2.com/research/sota/protein-pocket-generation-on-crossdocked-test.md?metric=Salt%20Bridges>): Higher is better; unit: SCALAR.

- [Hydrophobic Interactions](<https://www.sota2.com/research/sota/protein-pocket-generation-on-crossdocked-test.md?metric=Hydrophobic%20Interactions>): Higher is better; unit: SCALAR.

- [Pi-Pi Stacking](<https://www.sota2.com/research/sota/protein-pocket-generation-on-crossdocked-test.md?metric=Pi-Pi%20Stacking>): Higher is better; unit: SCALAR.

## Recorded results

| Method | Clash | Result date | Report paper |
| --- | --- | --- | --- |
| PocketFlow | 1.21 | Not recorded | 68fa5f601e209131ce9e96e3 |
| RFDiffusionAA | 3.58 | Not recorded | 68fa5f601e209131ce9e96e3 |
| Test set | 4.59 | Not recorded | 68fa5f601e209131ce9e96e3 |
| dyMEAN | 4.65 | Not recorded | 68fa5f601e209131ce9e96e3 |
| FAIR | 4.9 | Not recorded | 68fa5f601e209131ce9e96e3 |
| DEPACT | 6.72 | Not recorded | 68fa5f601e209131ce9e96e3 |

### PocketFlow

Clash: 1.21. Result ID: 698bc5ce7a967eddb7713fed.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f601e209131ce9e96e3.md>)

[Method origin paper](<https://www.sota2.com/research/paper/68fa5f601e209131ce9e96e3.md>)

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

### RFDiffusionAA

Clash: 3.58. Result ID: 698bc5ce7a967eddb7713fec.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f601e209131ce9e96e3.md>)

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

### Test set

Clash: 4.59. Result ID: 698bc5ce7a967eddb7713fe8.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f601e209131ce9e96e3.md>)

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

### dyMEAN

Clash: 4.65. Result ID: 698bc5ce7a967eddb7713fea.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f601e209131ce9e96e3.md>)

[Method origin paper](<https://www.sota2.com/research/paper/68fa5f421e209131ce9e87e6.md>)

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

### FAIR

Clash: 4.9. Result ID: 698bc5ce7a967eddb7713feb.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f601e209131ce9e96e3.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.

### DEPACT

Clash: 6.72. Result ID: 698bc5ce7a967eddb7713fe9.

[Reporting paper](<https://www.sota2.com/research/paper/68fa5f601e209131ce9e96e3.md>)

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

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