Protocol

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

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

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 SJC; Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall; Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall; Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall; Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC test split Recall

4 evaluations · 16 metric rows

At a glance

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.

How it works

Evaluation in this paper

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

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

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

Comparison and metric

SJC test split · Recall

Recall (unitless) · Higher values are better for this metric.

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

Evaluation protocol · SJC test split

P2Rank · Configuration · Independent external evaluation0.660
GraphBind · Configuration · Independent external evaluation0.568 ± 0.024
DeepProSite · Configuration · Independent external evaluation0.458 ± 0.022
CLAPE-SMB · Configuration · Author-reported evaluation0.456 ± 0.006

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

Values, uncertainty and evidence

Recall: original source values
Tested entity	Printed value	Uncertainty	Evidence
P2Rank · Configuration	0.660 unitless	Not reported	Independent external evaluation · source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall
GraphBind · Configuration	0.568 ± 0.024 unitless	printed: 0.024; value: 0.024; type: not explicitly identified in inspected table or caption	Independent external evaluation · source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall
DeepProSite · Configuration	0.458 ± 0.022 unitless	printed: 0.022; value: 0.022; type: not explicitly identified in inspected table or caption	Independent external evaluation · source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall
CLAPE-SMB · Configuration	0.456 ± 0.006 unitless	printed: 0.006; value: 0.006; type: not explicitly identified in inspected table or caption	Author-reported evaluation · source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC test split Recall

Scope and limitations

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.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 4 evaluations · 16 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
CLAPE-SMB: SJC test split Configuration: CLAPE-SMBProtocol: SJC test split (protein-small molecule binding-site prediction)Dataset: SJC test split Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences. Author-reported evaluation · Evaluation metadata: needs review
0.651 ± 0.016 Precision Unit: unitless · Direction: higher	Uncertainty: printed: 0.016; value: 0.016; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 5 CLAPE-SMB, column 3: SJC test split Precision Source checking is not independent reproduction.
0.529 ± 0.004 MCC Unit: unitless · Direction: higher	Uncertainty: printed: 0.004; value: 0.004; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 5 CLAPE-SMB, column 4: SJC test split MCC Source checking is not independent reproduction.
0.915 ± 0.002 AUROC Unit: unitless · Direction: higher	Uncertainty: printed: 0.002; value: 0.002; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 5 CLAPE-SMB, column 5: SJC test split AUROC Source checking is not independent reproduction.
0.456 ± 0.006 Recall Unit: unitless · Direction: higher	Uncertainty: printed: 0.006; value: 0.006; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC test split Recall Source checking is not independent reproduction.
P2Rank: SJC test split Configuration: P2RankProtocol: SJC test split (protein-small molecule binding-site prediction)Dataset: SJC test split Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences. Independent external evaluation · Evaluation metadata: needs review
0.660 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall Source checking is not independent reproduction.
0.293 MCC Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 2 P2Rank, column 4: SJC test split MCC Source checking is not independent reproduction.
N/A AUROC Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 2 P2Rank, column 5: SJC test split AUROC Source checking is not independent reproduction.
0.180 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 2 P2Rank, column 3: SJC test split Precision Source checking is not independent reproduction.
GraphBind: SJC test split Configuration: GraphBindProtocol: SJC test split (protein-small molecule binding-site prediction)Dataset: SJC test split Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences. Independent external evaluation · Evaluation metadata: needs review
0.486 ± 0.005 MCC Unit: unitless · Direction: higher	Uncertainty: printed: 0.005; value: 0.005; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 3 GraphBind, column 4: SJC test split MCC Source checking is not independent reproduction.
0.906 ± 0.003 AUROC Unit: unitless · Direction: higher	Uncertainty: printed: 0.003; value: 0.003; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 3 GraphBind, column 5: SJC test split AUROC Source checking is not independent reproduction.
0.568 ± 0.024 Recall Unit: unitless · Direction: higher	Uncertainty: printed: 0.024; value: 0.024; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall Source checking is not independent reproduction.
0.462 ± 0.011 Precision Unit: unitless · Direction: higher	Uncertainty: printed: 0.011; value: 0.011; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 3 GraphBind, column 3: SJC test split Precision Source checking is not independent reproduction.
DeepProSite: SJC test split Configuration: DeepProSiteProtocol: SJC test split (protein-small molecule binding-site prediction)Dataset: SJC test split Residue-level small-molecule binding-site classification. 80/10/10 train/validation/test partition of nonredundant sequences. Independent external evaluation · Evaluation metadata: needs review
0.458 ± 0.022 Recall Unit: unitless · Direction: higher	Uncertainty: printed: 0.022; value: 0.022; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall Source checking is not independent reproduction.
0.926 ± 0.002 AUROC Unit: unitless · Direction: higher	Uncertainty: printed: 0.002; value: 0.002; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 4 DeepProSite, column 5: SJC test split AUROC Source checking is not independent reproduction.
0.524 ± 0.015 MCC Unit: unitless · Direction: higher	Uncertainty: printed: 0.015; value: 0.015; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 4 DeepProSite, column 4: SJC test split MCC Source checking is not independent reproduction.
0.644 ± 0.011 Precision Unit: unitless · Direction: higher	Uncertainty: printed: 0.011; value: 0.011; type: not explicitly identified in inspected table or caption Scored: Not reported · Eligible: Not reported	source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 3 (Tab3), row 4 DeepProSite, column 3: SJC test split Precision Source checking is not 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

What is still missing

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 SJC; Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall; Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall; Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall; Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC test split Recall

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

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-07cf559d2f1f9262e7

Evidence table

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 2026-09-17-d277315f7d76
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 SJC; Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall; Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall; Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall; Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC 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 SJC 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 SJC; Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall; Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall; Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall; Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC 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 SJC; Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall; Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall; Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall; Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC 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-419681a9f3306b9e0e Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

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-07cf559d2f1f9262e7

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-tab3-recall; title: SJC test split · Recall; protocol id: paper-protocol-07cf559d2f1f9262e7; dataset id: paper-dataset-623c309e2fb4d39ef8; metric: Recall; unit: unitless; direction: higher; result ids: paper-result-3c8603f3a617ae353d; paper-result-b455cc6c453819bf59; paper-result-86b3e09746a262c729; paper-result-f678244aa5db050c82; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models on the SJC; Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall; Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall; Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall; Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC 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-tab3-precision; title: SJC test split · Precision; protocol id: paper-protocol-07cf559d2f1f9262e7; dataset id: paper-dataset-623c309e2fb4d39ef8; metric: Precision; unit: unitless; direction: higher; result ids: paper-result-c76919342c3926a7e8; paper-result-c04870d60a021ac0ed; paper-result-fcf6afead98be8b7bc; paper-result-02b4a5a19b61ad5217; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models on the SJC; Table 3 (Tab3), row 2 P2Rank, column 3: SJC test split Precision; Table 3 (Tab3), row 3 GraphBind, column 3: SJC test split Precision; Table 3 (Tab3), row 4 DeepProSite, column 3: SJC test split Precision; Table 3 (Tab3), row 5 CLAPE-SMB, column 3: SJC 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-tab3-mcc; title: SJC test split · MCC; protocol id: paper-protocol-07cf559d2f1f9262e7; dataset id: paper-dataset-623c309e2fb4d39ef8; metric: MCC; unit: unitless; direction: higher; result ids: paper-result-63c3e75a69cfad040e; paper-result-42d845442e40d9846c; paper-result-bafeb53a23564fc9e5; paper-result-936e56c8fad08e6191; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models on the SJC; Table 3 (Tab3), row 2 P2Rank, column 4: SJC test split MCC; Table 3 (Tab3), row 3 GraphBind, column 4: SJC test split MCC; Table 3 (Tab3), row 4 DeepProSite, column 4: SJC test split MCC; Table 3 (Tab3), row 5 CLAPE-SMB, column 4: SJC 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-tab3-auroc; title: SJC test split · AUROC; protocol id: paper-protocol-07cf559d2f1f9262e7; dataset id: paper-dataset-623c309e2fb4d39ef8; metric: AUROC; unit: unitless; direction: higher; result ids: paper-result-a1b671f27b279cb8b3; paper-result-afdce2cee34b41cf09; paper-result-87d8d792a85dd7223d; paper-result-a337f472f62cd0d12a; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models on the SJC; Table 3 (Tab3), row 2 P2Rank, column 5: SJC test split AUROC; Table 3 (Tab3), row 3 GraphBind, column 5: SJC test split AUROC; Table 3 (Tab3), row 4 DeepProSite, column 5: SJC test split AUROC; Table 3 (Tab3), row 5 CLAPE-SMB, column 5: SJC 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 SJC; Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall; Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall; Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall; Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC 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 SJC; Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall; Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall; Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall; Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC test split Recall; ambiguities: None recorded

Related records

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

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