BioBench Atlas
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paper · benchmark creator

PPB-Affinity: Protein-Protein Binding Affinity dataset for AI-based protein drug discovery

Artificial Intelligence Innovation Center, Research Institute of Tsinghua, Pearl River Delta · Cyagen Biosciences (Suzhou) Inc. · Cyagen Biosciences (Guangzhou) Inc. · Cyagen Biomodels (Guangzhou) Co., Ltd · Department of Pain Medicine, Shenzhen Nanshan People’s Hospital, Shenzhen University Medical School · 2024-12-03

Relationship layer

Benchmark usage

This table records what the work did with each benchmark before attempting to normalize a run. Partial claims remain visible without being treated as comparable evaluations.

benchmark creation

ppb-affinity-protein-protein-binding-affinity-dataset-ppb-affinity-1-use

Non-evaluationunknown

Benchmark: PPB-Affinity · version Not reported

Selection
not applicable
Models
Not reported / not applicable
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: No formal PPB-Affinity version label is printed.; The exact dataset release date is not printed; the data citation reports only 2024.; The licenses of the two GitHub repositories are not printed.; Figure 3 raster content is unavailable locally, preventing inspection of any additional labeled partition values.

AI-assisted double-pass extraction; values are limited to independently supported claims.

Evidence
  • section: Background & Summary, paragraph 4
    Supports: /relation_type
  • section: Background & Summary, paragraph 4
    Supports: /benchmark_id

evaluation

ppb-affinity-protein-protein-binding-affinity-dataset-ppb-affinity-2-use

Partialunknown

Benchmark: PPB-Affinity · version Not reported

Selection
not reported
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: The testing-subset size and selection procedure are not printed in the available text.; Repeats, seed, train-validation-test partition sizes, and model version are not reported in the available text.; Linked Figures 4–5 are unavailable locally, so additional labeled subgroup and source-partition results could not be inspected.; benchmark version; realized n/scope; metric; numeric result; prompt and tools; grader and repeats

Owner-reviewed conservative publication: the creator evaluation is retained only as a partial relationship; conflicted settings and outcomes are omitted pending manual reconciliation.

Evidence
  • section: Technical Validation > Whole dataset, paragraph 47
    Supports: /relation_type
  • section: Abstract, paragraph 1
    Supports: /benchmark_id
  • section: Author contributions; Technical Validation > A benchmark affinity prediction, paragraph 46
    Supports: /model_ids

training

ppb-affinity-protein-protein-binding-affinity-dataset-ppb-affinity-3-use

Non-evaluationunknown

Benchmark: PPB-Affinity · version Not reported

Selection
not applicable
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: The training percentages shown in Figure 5F cannot be inspected because the linked raster is unavailable locally.; Training sample counts, split procedure, repeats, seed, hyperparameters, and model version are not reported in the available text.

AI-assisted double-pass extraction; values are limited to independently supported claims.

Evidence
  • section: Technical Validation > Source datasets, paragraph 50
    Supports: /relation_type
  • section: Abstract, paragraph 1; Technical Validation > Source datasets, paragraph 50
    Supports: /benchmark_id
  • section: Technical Validation > Source datasets, paragraph 50
    Supports: /scope
  • section: Author contributions; Technical Validation > A benchmark affinity prediction, paragraph 46; Source datasets, paragraph 50
    Supports: /model_ids

Normalized evaluation runs

This source has no normalized model run. It may be a creator-only source or a partial/non-evaluation benchmark use.