# Protein Pocket Design on PPDBench (test)

Source: [Protein Pocket Design on PPDBench (test)](<https://www.sota2.com/research/sota/protein-pocket-design-on-ppdbench-test>)

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

Data updated: 2026-02-26T05:21:23.574Z

Evaluation of models for Protein Pocket Design using metrics such as AAR, scRMSD, and ΔΔG on the test split of the PPDBench dataset.

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) | PPDBench (test) |
| Metric | AAR |
| Unit | PERCENT |
| Direction | Higher is better |
| Results loaded | 8 of 8 |
| 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

- [AAR](<https://www.sota2.com/research/sota/protein-pocket-design-on-ppdbench-test.md?metric=AAR>): Higher is better; unit: PERCENT.

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

- [ΔΔG](<https://www.sota2.com/research/sota/protein-pocket-design-on-ppdbench-test.md?metric=%CE%94%CE%94G>): Lower is better; unit: SCALAR.

## Recorded results

| Method | AAR | Result date | Report paper |
| --- | --- | --- | --- |
| PocketFlow | 48.19 | Not recorded | 68fa5f601e209131ce9e96e3 |
| PocketFlow (w/o Aff Guide) | 47.78 | Not recorded | 68fa5f601e209131ce9e96e3 |
| PocketFlow (w/o Geo Guide) | 47.3 | Not recorded | 68fa5f601e209131ce9e96e3 |
| RFDiffusionAA | 46.85 | Not recorded | 68fa5f601e209131ce9e96e3 |
| PocketFlow (w/o Geo & Aff Guide) | 44.63 | Not recorded | 68fa5f601e209131ce9e96e3 |
| PocketFlow (w/o Inter Learning) | 36.41 | Not recorded | 68fa5f601e209131ce9e96e3 |
| FAIR | 32.53 | Not recorded | 68fa5f601e209131ce9e96e3 |
| dyMEAN | 26.29 | Not recorded | 68fa5f601e209131ce9e96e3 |

### PocketFlow

AAR: 48.19. Result ID: 698bc5ce7a967eddb7713ff1.

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

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

Recorded evaluation configuration: {"Affinity Guidance":"true","Interaction Geometry Guidance":"true","Interaction Learning":"true"}. This record does not assert independent reproduction.

### PocketFlow (w/o Aff Guide)

AAR: 47.78. Result ID: 698bc5ce7a967eddb7713ff2.

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

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

Recorded evaluation configuration: {"Affinity Guidance":"false","Interaction Geometry Guidance":"true","Interaction Learning":"true"}. This record does not assert independent reproduction.

### PocketFlow (w/o Geo Guide)

AAR: 47.3. Result ID: 698bc5ce7a967eddb7713ff3.

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

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

Recorded evaluation configuration: {"Affinity Guidance":"true","Interaction Geometry Guidance":"false","Interaction Learning":"true"}. This record does not assert independent reproduction.

### RFDiffusionAA

AAR: 46.85. Result ID: 698bc5ce7a967eddb7713ff0.

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

Recorded evaluation configuration: {"Checkpoint":"\[1\]"}. This record does not assert independent reproduction.

### PocketFlow (w/o Geo & Aff Guide)

AAR: 44.63. Result ID: 698bc5ce7a967eddb7713ff4.

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

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

Recorded evaluation configuration: {"Affinity Guidance":"false","Interaction Geometry Guidance":"false","Interaction Learning":"true"}. This record does not assert independent reproduction.

### PocketFlow (w/o Inter Learning)

AAR: 36.41. Result ID: 698bc5ce7a967eddb7713ff5.

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

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

Recorded evaluation configuration: {"Affinity Guidance":"true","Interaction Geometry Guidance":"false","Interaction Learning":"false"}. This record does not assert independent reproduction.

### FAIR

AAR: 32.53. Result ID: 698bc5ce7a967eddb7713fef.

[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: {"Pre-training":"protein-small molecule datasets"}. This record does not assert independent reproduction.

### dyMEAN

AAR: 26.29. Result ID: 698bc5ce7a967eddb7713fee.

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

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

Recorded evaluation configuration: {"Pre-training":"protein-small molecule datasets"}. This record does not assert independent reproduction.

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