PFMBench BINDING-DB: BindingDB
BindingDB. Scored with Spearman on BindingDB. Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.
Overview
BindingDB. Scored with Spearman on BindingDB. Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
PFMBench BINDING-DB: BindingDB
spearman (correlation) · Higher values are better.
PFMBench BINDING-DB: BindingDB · BindingDB (PFMBench split)
Evidence origin: Author-reported evaluation.
pfmbench primary benchmark evidence · Table 1, row(BindingDB)- The metric differs by task, taken from Table 1, so these figures cannot be averaged into one score.
- Table 3 scores come from adapter fine-tuning; the ProteinGym figure is zero-shot and is not comparable to them.
Comparison details and limitations
Every method PFMBench reports on BindingDB, scored with Spearman on BindingDB.
- Author-reported numbers, source checked but not independently reproduced.
Automated source review: 2026-09-18. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 12 of 12 matching rows.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- DPLM on PFMBench BINDING-DB: BindingDB
- ESM-2 on PFMBench BINDING-DB: BindingDB
- ESM-C on PFMBench BINDING-DB: BindingDB
- ESM3 on PFMBench BINDING-DB: BindingDB
- PGLM on PFMBench BINDING-DB: BindingDB
- ProstT5 on PFMBench BINDING-DB: BindingDB
- ProtGPT2 on PFMBench BINDING-DB: BindingDB
- ProTrek on PFMBench BINDING-DB: BindingDB
- ProtST on PFMBench BINDING-DB: BindingDB
- ProtT5 on PFMBench BINDING-DB: BindingDB
- SaProt on PFMBench BINDING-DB: BindingDB
- VenusPLM on PFMBench BINDING-DB: BindingDB
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-pfmbench Individual claims | pfmbench primary benchmark evidence Table 1, row(BindingDB) Version: 2506.14796v1 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: pfmbench-association-binding-db Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: source checked
1 source records and release history
- pfmbench primary benchmark evidence · Original source · 2506.14796v1
Technical metadata and extraction receipts
Stable ID: pfmbench-task-binding-db
- areas
- proteins-complexes
- tasks
- BindingDB
- metric
- Spearman
- metric direction
- higher
- dataset
- BindingDB
- protocol
- Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.
- source locator
- Table 1, row(BindingDB)
- comparison panels
- id: pfmbench-panel-binding-db; title: PFMBench BINDING-DB: BindingDB; protocol id: pfmbench-task-binding-db; dataset id: pfmbench-dataset-bindingdb; metric: spearman; unit: correlation; direction: higher; result ids: pfmbench-result-esm-2-binding-db-spearman; pfmbench-result-venusplm-binding-db-spearman; pfmbench-result-esm-c-binding-db-spearman; pfmbench-result-protgpt2-binding-db-spearman; pfmbench-result-pglm-binding-db-spearman; pfmbench-result-prott5-binding-db-spearman; pfmbench-result-dplm-binding-db-spearman; pfmbench-result-saprot-binding-db-spearman; pfmbench-result-prostt5-binding-db-spearman; pfmbench-result-protst-binding-db-spearman; pfmbench-result-esm3-binding-db-spearman; pfmbench-result-protrek-binding-db-spearman; source ids: expansion-p3-pfmbench; source locator: Table 1, row(BindingDB); context: Every method PFMBench reports on BindingDB, scored with Spearman on BindingDB.; caveats: Author-reported numbers, source checked but not independently reproduced.; The metric differs by task, taken from Table 1, so these figures cannot be averaged into one score.; Table 3 scores come from adapter fine-tuning; the ProteinGym figure is zero-shot and is not comparable to them.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: PFMBench
- subject: PFMBench BINDING-DB: part of discovery-benchmark-pfmbench
- benchmark: DPLM on PFMBench BINDING-DB: BindingDB
- benchmark: ESM-2 on PFMBench BINDING-DB: BindingDB
- benchmark: ESM-C on PFMBench BINDING-DB: BindingDB
- benchmark: ESM3 on PFMBench BINDING-DB: BindingDB
- benchmark: PGLM on PFMBench BINDING-DB: BindingDB
- benchmark: ProstT5 on PFMBench BINDING-DB: BindingDB
- benchmark: ProtGPT2 on PFMBench BINDING-DB: BindingDB
- benchmark: ProTrek on PFMBench BINDING-DB: BindingDB
- benchmark: ProtST on PFMBench BINDING-DB: BindingDB
- benchmark: ProtT5 on PFMBench BINDING-DB: BindingDB
- benchmark: SaProt on PFMBench BINDING-DB: BindingDB
- benchmark: VenusPLM on PFMBench BINDING-DB: BindingDB