Protocol

UniProtSMB test split (protein-small molecule binding-site prediction)

UniProtSMB test split · Recall. Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences.

Sources

Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall

4 evaluations · 16 results

Overview

Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.

limited source coverage · Automated source review, 2026-09-17. All specifications and missing details

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

Evaluation scope and datasetMetric and reported setup

UniProtSMB test split · Recall

Recall (unitless) · Higher values are better.

UniProtSMB test split (protein-small molecule binding-site prediction) · UniProtSMB test split

Evidence origin: Independent external evaluation, Author-reported evaluation.

Sequence-only and structure-using predictors have unequal input information and are labelled method comparisons, not architecture-controlled tests. CLAPE-SMB seeds 6,17,35,42; the table prints ± but does not explicitly label the spread in its caption. N/A AUROC remains unavailable. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.

Comparison details and limitations

Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences.

Automated source review: 2026-09-17. 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.

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Tested configuration

00.250.50.751

Reported score

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Evaluation in this paper

Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences.

Sources

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Tasks

protein-small molecule binding-site prediction

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Recorded evaluations

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Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

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Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Training-set class prior where supervised fitting is permitted

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Regularised classifier on simple permitted features, or protocol's conventional reference

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

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Limitations and conditions

No source-reviewed explanatory claims are recorded here yet.

Profile review details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Stable record: paper-protocol-89b76bfabd1dfe31a6

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Datasets	Not extracted or verified for this record.
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Splits	Not extracted or verified for this record.
Allowed inputs	Not extracted or verified for this record.
Adaptation	Not extracted or verified for this record.
Metrics	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Papers and result coverage

Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.

Paper or primary resource	Version	Reference
Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning	version of record	Read source DOI: 10.1186/s13321-024-00920-2

Historical gaps recorded on 2026-09-17

The catalogue now holds 16 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.

exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.

Search and extraction details

complete tables extracted

Searches

Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning 10.1186/s13321-024-00920-2

Evidence locations

Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall

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.

3 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Evaluation in this paper Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Introduction UniProtSMB test split · Recall. Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.summary` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: evaluates task reported-task-b181ed450cdd41 Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-17 Audit details Field: `links:evaluates_task:reported-task-b181ed450cdd41` Claim: paper-claim-3a8502ecc836c7589d Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: needs review

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Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Original source · version of record

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Technical metadata and extraction receipts

Stable ID: paper-protocol-89b76bfabd1dfe31a6

areas: proteins-complexes
tasks: protein-small molecule binding-site prediction
entity level: protocol
protocol: Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences.
comparison panels: id: clape-smb-2024-tab4-recall; title: UniProtSMB test split · Recall; protocol id: paper-protocol-89b76bfabd1dfe31a6; dataset id: paper-dataset-7ed13bec749f1e245b; metric: Recall; unit: unitless; direction: higher; result ids: paper-result-a52e839c67a23202a9; paper-result-1fef4fca1431b14c73; paper-result-08de771b9d631cbb90; paper-result-114f60a38e97139e57; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall; context: Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences.; caveats: Sequence-only and structure-using predictors have unequal input information and are labelled method comparisons, not architecture-controlled tests. CLAPE-SMB seeds 6,17,35,42; the table prints ± but does not explicitly label the spread in its caption. N/A AUROC remains unavailable. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: clape-smb-2024-tab4-precision; title: UniProtSMB test split · Precision; protocol id: paper-protocol-89b76bfabd1dfe31a6; dataset id: paper-dataset-7ed13bec749f1e245b; metric: Precision; unit: unitless; direction: higher; result ids: paper-result-9d84f8da0854369c5c; paper-result-ba1e3a15b41c7f68e7; paper-result-a1f27fb075923f53e8; paper-result-0cb8ce6c55a8f0597f; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 3: UniProtSMB test split Precision; Table 4 (Tab4), row 3 GraphBind, column 3: UniProtSMB test split Precision; Table 4 (Tab4), row 4 DeepProSite, column 3: UniProtSMB test split Precision; Table 4 (Tab4), row 5 CLAPE-SMB, column 3: UniProtSMB test split Precision; context: Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences.; caveats: Sequence-only and structure-using predictors have unequal input information and are labelled method comparisons, not architecture-controlled tests. CLAPE-SMB seeds 6,17,35,42; the table prints ± but does not explicitly label the spread in its caption. N/A AUROC remains unavailable. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: clape-smb-2024-tab4-mcc; title: UniProtSMB test split · MCC; protocol id: paper-protocol-89b76bfabd1dfe31a6; dataset id: paper-dataset-7ed13bec749f1e245b; metric: MCC; unit: unitless; direction: higher; result ids: paper-result-7ed2311155bd397324; paper-result-de34ece35da8021e97; paper-result-ba078e213fdac2e0bf; paper-result-90ff2ad95b57c8f0f6; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 4: UniProtSMB test split MCC; Table 4 (Tab4), row 3 GraphBind, column 4: UniProtSMB test split MCC; Table 4 (Tab4), row 4 DeepProSite, column 4: UniProtSMB test split MCC; Table 4 (Tab4), row 5 CLAPE-SMB, column 4: UniProtSMB test split MCC; context: Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences.; caveats: Sequence-only and structure-using predictors have unequal input information and are labelled method comparisons, not architecture-controlled tests. CLAPE-SMB seeds 6,17,35,42; the table prints ± but does not explicitly label the spread in its caption. N/A AUROC remains unavailable. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: clape-smb-2024-tab4-auroc; title: UniProtSMB test split · AUROC; protocol id: paper-protocol-89b76bfabd1dfe31a6; dataset id: paper-dataset-7ed13bec749f1e245b; metric: AUROC; unit: unitless; direction: higher; result ids: paper-result-7011ff11e364052ff1; paper-result-195480a469229de195; paper-result-d0fa42d3c13fe8ec4d; paper-result-e4602df92496bbb342; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 5: UniProtSMB test split AUROC; Table 4 (Tab4), row 3 GraphBind, column 5: UniProtSMB test split AUROC; Table 4 (Tab4), row 4 DeepProSite, column 5: UniProtSMB test split AUROC; Table 4 (Tab4), row 5 CLAPE-SMB, column 5: UniProtSMB test split AUROC; context: Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences.; caveats: Sequence-only and structure-using predictors have unequal input information and are labelled method comparisons, not architecture-controlled tests. CLAPE-SMB seeds 6,17,35,42; the table prints ± but does not explicitly label the spread in its caption. N/A AUROC remains unavailable. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17
benchmark research: review date: 2026-09-17; status: complete_tables_extracted; primary sources: clape-smb-2024; inspected locators: Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall; searched queries: Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning 10.1186/s13321-024-00920-2; gaps: exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall; ambiguities: None recorded

Related records

evaluates task: protein-small molecule binding-site prediction
subject: UniProtSMB test split (protein-small molecule binding-site prediction): links:evaluates_task:reported-task-b181ed450cdd41
benchmark: P2Rank: UniProtSMB test split
benchmark: CLAPE-SMB: UniProtSMB test split
benchmark: GraphBind: UniProtSMB test split
benchmark: DeepProSite: UniProtSMB test split

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