BIPSPI, sequence-only (ATOM3D baseline)
Sequence-only BIPSPI, a boosted decision tree method for protein interaction prediction, as the ATOM3D text describes it.
Overview
Sequence-only BIPSPI, a boosted decision tree method for protein interaction prediction, as the ATOM3D text describes it.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: BIPSPI, sequence-only (ATOM3D baseline) (cited as [Sanchez-Garcia et al., 2018]) | Task: ATOM3D PIP: Protein interface prediction Dataset subset: ATOM3D PIP (ATOM3D split) | 0.841 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBIPSPI, sequence-only (ATOM3D baseline) on ATOM3D PIP: Protein interface prediction Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(PIP AUROC), column([Sanchez-Garcia et al., 2018]) |
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Evidence
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Sources and history
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Release 2026-09-29-06401fd5b220 · Record review: source checked
2 source records and release history
- ATOM3D: Tasks On Molecules in Three Dimensions · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
- BIPSPI: a method for the prediction of partner-specific protein–protein interfaces (PMC6361243) · Original source · PMC6361243
Technical metadata and extraction receipts
Stable ID: atom3d-method-sanchez-garcia-et-al-2018
- areas
- molecular-interactions
- source locator
- Table 4, column([Sanchez-Garcia et al., 2018])
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
- source label
- [Sanchez-Garcia et al., 2018]
- source identity
- status: resolved; label form: bracketed_citation; display name: BIPSPI, sequence-only (ATOM3D baseline); identity: BIPSPI; configuration: Sequence-only BIPSPI using sequence and conservation features, evaluated on DB5.; basis: ATOM3D §5.1 compares to 'the sequence-only version of BIPSPI [Sanchez-Garcia et al., 2018]', and App. F.2 uses 'their model that uses only sequence and sequence conservation features and is evaluated on DB5'. BIPSPI Table 1 reports sequence-only ('Seq') variants.; source ids: evidence-expansion-atom3d-92656c20; source-label-bipspi-pmc-c4c9bf4b; source locator: ATOM3D arXiv:2012.04035v4 §5.1 and Table 4, p.7; App. F.2, p.24; Table 8 PIP row, p.28. BIPSPI, Bioinformatics 35(3):470 (PMC6361243), Table 1, Input 'Seq' rows.; known details: label: Features; value: Sequence and sequence conservation features only.; source ids: evidence-expansion-atom3d-92656c20; source locator: ATOM3D App. F.2, p.24; unknown: label: Who produced the value; note: The 0.841 AUROC does not appear in BIPSPI Table 1. ATOM3D does not say whether it retrained BIPSPI or took the value from elsewhere.; label: Checkpoint; note: No checkpoint or implementation revision is identified.; original name: [Sanchez-Garcia et al., 2018]; original description: Sequence-only BIPSPI, a boosted decision tree method for protein interaction prediction, as the ATOM3D text describes it.; review: method: automated_source_review; date: 2026-09-24; note: AI-assisted review against the cited primary sources. No human scientific review. Values, locators and comparison conditions are unchanged.