# Small-molecule-binding protein pocket design on CrossDocked (test)

Source: [Small-molecule-binding protein pocket design on CrossDocked (test)](<https://www.sota2.com/research/sota/small-molecule-binding-protein-pocket-design-on-crossdocked-test>)

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

Data updated: 2026-02-26T06:11:20.141Z

Evaluation of models designed for small-molecule binding to protein pockets using the CrossDocked test set, focusing on structural accuracy (scRMSD, AAR) and predicted binding affinity (Vina).

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 | Small-molecule-binding protein pocket design |
| Dataset (including any stated split) | CrossDocked (test) |
| Metric | scRMSD |
| Unit | SCALAR |
| Direction | Lower is better |
| Results loaded | 10 of 10 |
| 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

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

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

- [Vina Affinity](<https://www.sota2.com/research/sota/small-molecule-binding-protein-pocket-design-on-crossdocked-test.md?metric=Vina%20Affinity>): Lower is better; unit: SCALAR.

## Recorded results

| Method | scRMSD | Result date | Report paper |
| --- | --- | --- | --- |
| Test set | 0.65 | Not recorded | 68fa5f601e209131ce9e96e3 |
| PocketFlow | 0.65 | Not recorded | 68fa5f601e209131ce9e96e3 |
| PocketFlow | 0.66 | Not recorded | 68fa5f601e209131ce9e96e3 |
| PocketFlow | 0.67 | Not recorded | 68fa5f601e209131ce9e96e3 |
| RFDiffusionAA | 0.68 | Not recorded | 68fa5f601e209131ce9e96e3 |
| PocketFlow | 0.68 | Not recorded | 68fa5f601e209131ce9e96e3 |
| PocketFlow | 0.71 | Not recorded | 68fa5f601e209131ce9e96e3 |
| DEPACT | 0.73 | Not recorded | 68fa5f601e209131ce9e96e3 |
| FAIR | 0.75 | Not recorded | 68fa5f601e209131ce9e96e3 |
| dyMEAN | 0.79 | Not recorded | 68fa5f601e209131ce9e96e3 |

### Test set

scRMSD: 0.65. Result ID: 698bc5ce7a967eddb7714000.

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

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

### PocketFlow

scRMSD: 0.65. Result ID: 698bc5ce7a967eddb7714006.

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

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

Recorded evaluation configuration: {"Ablation":"w/o Aff Guide"}. This record does not assert independent reproduction.

### PocketFlow

scRMSD: 0.66. Result ID: 698bc5ce7a967eddb7714009.

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

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

Recorded evaluation configuration: {"Ablation":"w/o Inter Learning"}. This record does not assert independent reproduction.

### PocketFlow

scRMSD: 0.67. Result ID: 698bc5ce7a967eddb7714005.

[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

scRMSD: 0.68. Result ID: 698bc5ce7a967eddb7714004.

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

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

### PocketFlow

scRMSD: 0.68. Result ID: 698bc5ce7a967eddb7714007.

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

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

Recorded evaluation configuration: {"Ablation":"w/o Geo Guide"}. This record does not assert independent reproduction.

### PocketFlow

scRMSD: 0.71. Result ID: 698bc5ce7a967eddb7714008.

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

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

Recorded evaluation configuration: {"Ablation":"w/o Geo & Aff Guide"}. This record does not assert independent reproduction.

### DEPACT

scRMSD: 0.73. Result ID: 698bc5ce7a967eddb7714001.

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

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

### FAIR

scRMSD: 0.75. Result ID: 698bc5ce7a967eddb7714003.

[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.

### dyMEAN

scRMSD: 0.79. Result ID: 698bc5ce7a967eddb7714002.

[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.

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