BioBench Atlas
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preprint · independent reproduction

Explainable protein-protein binding affinity prediction via fine-tuning protein language models

Department of Computer Science and Engineering, Shiv Nadar University, Delhi-NCR · School of Informatics, University of Edinburgh · EaStCHEM School of Chemistry, University of Edinburgh · 2026-04-01

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.

evaluation

explainable-protein-protein-binding-affinity-predictio-ab-bind-5-use

Partialsubset · n=272

Benchmark: AB-Bind · version Not reported

Selection
filtered · Removed parent-PDB overlap or identical antigen-antibody sequence-pair overlap with PPB-Affinity training data
Models
BALM-PPI
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: Benchmark version is not reported.; BALM-PPI provider and version are not explicitly reported.; benchmark version; metric; numeric result

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

Evidence
  • section: 2.3
    Supports: /relation_type
  • section: 2.3
    Supports: /benchmark_id
  • section: 2.3
    Supports: /scope
  • section: 2.3
    Supports: /scope
  • table: Table 1
    Supports: /scope
  • section: 2.3
    Supports: /scope
  • table: Table 1
    Supports: /model_ids

fine tuning

explainable-protein-protein-binding-affinity-predictio-ab-bind-6-use

Non-evaluationunknown

Benchmark: AB-Bind · version Not reported

Selection
not applicable · Few-shot 10%
Models
BALM-PPI
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: Benchmark version and exact realized training/evaluation n are not reported.; BALM-PPI provider and version are not explicitly reported.

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

Evidence
  • table: Table 1
    Supports: /relation_type
  • table: Table 1
    Supports: /benchmark_id
  • table: Table 1
    Supports: /scope
  • table: Table 1
    Supports: /scope
  • table: Table 1
    Supports: /scope
  • table: Table 1
    Supports: /model_ids

fine tuning

explainable-protein-protein-binding-affinity-predictio-ab-bind-7-use

Non-evaluationunknown

Benchmark: AB-Bind · version Not reported

Selection
not applicable · Few-shot 20%
Models
BALM-PPI
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: Benchmark version and exact realized training/evaluation n are not reported.; BALM-PPI provider and version are not explicitly reported.

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

Evidence
  • table: Table 1
    Supports: /relation_type
  • table: Table 1
    Supports: /benchmark_id
  • table: Table 1
    Supports: /scope
  • table: Table 1
    Supports: /scope
  • table: Table 1
    Supports: /scope
  • table: Table 1
    Supports: /model_ids

fine tuning

explainable-protein-protein-binding-affinity-predictio-ab-bind-8-use

Non-evaluationunknown

Benchmark: AB-Bind · version Not reported

Selection
not applicable · Few-shot 30%
Models
BALM-PPI
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: Benchmark version and exact realized training/evaluation n are not reported.; BALM-PPI provider and version are not explicitly reported.

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

Evidence
  • table: Table 1
    Supports: /relation_type
  • table: Table 1
    Supports: /benchmark_id
  • table: Table 1
    Supports: /scope
  • table: Table 1
    Supports: /scope
  • table: Table 1
    Supports: /scope
  • table: Table 1
    Supports: /model_ids

fine tuning

explainable-protein-protein-binding-affinity-predictio-abbibench-10-use

Non-evaluationunknown

Benchmark: AbBiBench · version Not reported

Selection
not applicable · Few-Shot 10%
Models
BALM-PPI
Metrics
RMSE
Linked runs
None

Not reported / unresolved: Benchmark version and exact realized training/evaluation n per assay are not reported.; BALM-PPI provider and version are not explicitly reported.

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

Evidence
  • table: Table S6
    Supports: /relation_type
  • table: Table S6
    Supports: /benchmark_id
  • section: 2.4
    Supports: /scope
  • section: 2.4
    Supports: /scope
  • table: Table S5
    Supports: /scope
  • table: Table S6
    Supports: /scope
  • table: Table S6
    Supports: /model_ids
  • table: Table S6
    Supports: /metric_labels

fine tuning

explainable-protein-protein-binding-affinity-predictio-abbibench-11-use

Non-evaluationunknown

Benchmark: AbBiBench · version Not reported

Selection
not applicable · Few-Shot 20%
Models
BALM-PPI
Metrics
RMSE
Linked runs
None

Not reported / unresolved: Benchmark version and exact realized training/evaluation n per assay are not reported.; BALM-PPI provider and version are not explicitly reported.

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

Evidence
  • table: Table S6
    Supports: /relation_type
  • table: Table S6
    Supports: /benchmark_id
  • section: 2.4
    Supports: /scope
  • section: 2.4
    Supports: /scope
  • table: Table S5
    Supports: /scope
  • table: Table S6
    Supports: /scope
  • table: Table S6
    Supports: /model_ids
  • table: Table S6
    Supports: /metric_labels

fine tuning

explainable-protein-protein-binding-affinity-predictio-abbibench-12-use

Non-evaluationunknown

Benchmark: AbBiBench · version Not reported

Selection
not applicable · Few-Shot 30%
Models
BALM-PPI
Metrics
RMSE
Linked runs
None

Not reported / unresolved: Benchmark version and exact realized training/evaluation n per assay are not reported.; BALM-PPI provider and version are not explicitly reported.

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

Evidence
  • table: Table S6
    Supports: /relation_type
  • table: Table S6
    Supports: /benchmark_id
  • section: 2.4
    Supports: /scope
  • section: 2.4
    Supports: /scope
  • table: Table S5
    Supports: /scope
  • table: Table S6
    Supports: /scope
  • table: Table S6
    Supports: /model_ids
  • table: Table S6
    Supports: /metric_labels

evaluation

explainable-protein-protein-binding-affinity-predictio-abbibench-9-use

Partialsubset · n=9

Benchmark: AbBiBench · version Not reported

Selection
filtered · Nine selected DMS assays: 1n8z, 1mhp_LC, 3gbn_h1, 3gbn_h9, 4fqi_h1, aayl49_ml, aayl50_LC, aayl51, aayl52
Models
BALM-PPI
Metrics
RMSE
Linked runs
None

Not reported / unresolved: Benchmark version is not reported.; The source reports assay inventories, but not an exact realized evaluation n for every assay.; BALM-PPI provider and version are not explicitly reported.; benchmark version

AI-assisted double-pass extraction; n=9 counts selected assay tracks, not individual examples. Values are limited to independently supported claims.

Evidence
  • section: 2.4
    Supports: /relation_type
  • section: 2.4
    Supports: /benchmark_id
  • section: 2.4
    Supports: /scope
  • section: 2.4
    Supports: /scope
  • table: Table S5
    Supports: /scope
  • table: Table S5
    Supports: /scope
  • table: Table S6
    Supports: /model_ids
  • table: Table S6
    Supports: /metric_labels

training

explainable-protein-protein-binding-affinity-predictio-ppb-affinity-1-use

Non-evaluationunknown

Benchmark: PPB-Affinity · version Not reported

Selection
not applicable
Models
BALM-PPI
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: Benchmark version is not reported.; Exact per-fold training sizes are not reported for cold and sequence-similarity splits.; BALM-PPI provider and version are not explicitly reported.

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

Evidence
  • section: 2.1
    Supports: /relation_type
  • section: 2.1
    Supports: /benchmark_id
  • section: 4.1 Dataset
    Supports: /scope
  • section: 4.1 Dataset
    Supports: /scope
  • table: Table S1
    Supports: /scope
  • section: 4.1 Dataset
    Supports: /scope
  • section: 2.1
    Supports: /model_ids

evaluation

explainable-protein-protein-binding-affinity-predictio-ppb-affinity-2-use

Partialsubset

Benchmark: PPB-Affinity · version Not reported

Selection
formal subset · Random five-fold cross-validation with 80% training and 20% testing per fold
Metrics
RMSE
Linked runs
None

Not reported / unresolved: Benchmark version is not reported.; The exact realized random-split test n is not reported; only approximately 2,404 per fold is stated.; Model providers and versions are not explicitly reported.; benchmark version; realized n/scope

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

Evidence
  • table: Table S2
    Supports: /relation_type
  • table: Table S1
    Supports: /benchmark_id
  • section: 4.2
    Supports: /scope
  • section: 4.2
    Supports: /scope
  • table: Table S2
    Supports: /model_ids
  • table: Table S2
    Supports: /model_ids
  • table: Table S2
    Supports: /model_ids
  • table: Table S2
    Supports: /metric_labels

evaluation

explainable-protein-protein-binding-affinity-predictio-ppb-affinity-3-use

Partialsubset

Benchmark: PPB-Affinity · version Not reported

Selection
formal subset · GroupKFold cold split grouping interactions by PDB ID
Metrics
RMSE
Linked runs
None

Not reported / unresolved: Benchmark version and exact realized test n are not reported.; Model providers and versions are not explicitly reported.; benchmark version; realized n/scope

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

Evidence
  • table: Table S2
    Supports: /relation_type
  • section: 2.2
    Supports: /benchmark_id
  • section: 4.2
    Supports: /scope
  • section: 4.2
    Supports: /scope
  • table: Table S2
    Supports: /model_ids
  • table: Table S2
    Supports: /model_ids
  • table: Table S2
    Supports: /model_ids
  • table: Table S2
    Supports: /metric_labels

evaluation

explainable-protein-protein-binding-affinity-predictio-ppb-affinity-4-use

Partialsubset

Benchmark: PPB-Affinity · version Not reported

Selection
formal subset · K-mer Jaccard clustering with K=3, 30% similarity threshold, and pair exclusion
Metrics
RMSE
Linked runs
None

Not reported / unresolved: Benchmark version and exact realized test n are not reported.; Model providers and versions are not explicitly reported.; benchmark version; realized n/scope

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

Evidence
  • table: Table S2
    Supports: /relation_type
  • section: 2.1
    Supports: /benchmark_id
  • section: 4.2
    Supports: /scope
  • section: 4.2
    Supports: /scope
  • table: Table S2
    Supports: /model_ids
  • table: Table S2
    Supports: /model_ids
  • table: Table S2
    Supports: /model_ids
  • table: Table S2
    Supports: /metric_labels

Normalized evaluation runs

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