Task

protein-small molecule binding-site prediction

Small-molecule binding-site classification evaluates residue predictions on structural and curated protein annotations.

Sources

Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages

12 evaluations · 45 metric rows

At a glance

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. 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	SJC combines sc-PDB, JOINED and COACH420; UniProtSMB supplies a separately curated binding-site dataset. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
Splits	UniProtSMB representative proteins are partitioned 80:10:10 for training, validation and testing. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
Metrics	Precision, recall, MCC, AUROC and AUPRC. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
Baselines	ESM-2 versus ProtBert embeddings and MLP/CNN/Transformer head ablations; some head/model comparisons use the test set. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
Leakage controls	Protein similarity clustering and cluster-aware split comparisons are described; ESM-2 pretraining sequences are not universally excluded. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
Uncertainty	Multiple random seeds are evaluated; the paper reports fold-averaged metrics and standard deviations for its robustness experiment. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
Entity type	Paper-specific computational evaluation protocol. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
Organisms	The SJC structural collections and UniProtSMB annotations are selected by binding-site evidence and protein redundancy. Their preparation sections and dataset tables do not summarize organism composition or define a species-specific test. · Not reported in inspected sources Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · SJC dataset preparation; UniProtSMB dataset preparation; Table 1
Assays	Curated protein–small-molecule binding-site annotations. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
Allowed inputs	Protein amino-acid sequences. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
Adaptation	Supervised residue-level predictor fitted on the training proteins. Sources Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages

How it works

How it worksComputational evaluation flow

Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.

Sources

Evaluation methodology

SJC combines sc-PDB, JOINED and COACH420; UniProtSMB supplies a separately curated binding-site dataset. UniProtSMB representative proteins are partitioned 80:10:10 for training, validation and testing. Precision, recall, MCC, AUROC and AUPRC. ESM-2 versus ProtBert embeddings and MLP/CNN/Transformer head ablations; some head/model comparisons use the test set. Protein similarity clustering and cluster-aware split comparisons are described; ESM-2 pretraining sequences are not universally excluded. Multiple random seeds are evaluated; the paper reports fold-averaged metrics and standard deviations for its robustness experiment.

Sources

Evaluation design

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

Protocols

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

Recorded evaluations

Each evaluation records what was tested and under which conditions.

CLAPE-SMB with ESM-2: protein-small molecule binding-site prediction

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

COACH420, trained on CHEN11 · Recall

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

Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test.

Evaluation protocol · COACH420, trained on CHEN11

P2Rank · Configuration · Result quoted from another source0.888
GraphBind · Configuration · Result quoted from another source0.477
CLAPE-SMB · Configuration · Author-reported evaluation0.395 ± 0.066

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.

Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Comparison of CLAPE-SMB with other models trained on CHEN11 and tested on COACH420; Table 2 (Tab2), row 2 P2Rank, column 2: COACH420, trained on CHEN11 Recall; Table 2 (Tab2), row 3 GraphBind, column 2: COACH420, trained on CHEN11 Recall; Table 2 (Tab2), row 4 CLAPE-SMB, column 2: COACH420, trained on CHEN11 Recall

Values, uncertainty and evidence

Recall: original source values
Tested entity	Printed value	Uncertainty	Evidence
P2Rank · Configuration	0.888 unitless	Not reported	Result quoted from another source · source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 2 (Tab2), row 2 P2Rank, column 2: COACH420, trained on CHEN11 Recall
GraphBind · Configuration	0.477 unitless	Not reported	Result quoted from another source · source checkedProtein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Table 2 (Tab2), row 3 GraphBind, column 2: COACH420, trained on CHEN11 Recall
CLAPE-SMB · Configuration	0.395 ± 0.066 unitless	printed: 0.066; value: 0.066; 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 2 (Tab2), row 4 CLAPE-SMB, column 2: COACH420, trained on CHEN11 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 · 12 evaluations · 45 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 with ESM-2: protein-small molecule binding-site prediction Pipeline: CLAPE-SMB with ESM-2Task: protein-small molecule binding-site predictionDataset: SJC Contrastive CLAPE-SMB binding-site predictor with ESM-2 feature extractor Author-reported evaluation · Evaluation metadata: needs review
0.917 AUROC Unit: fraction · Direction: unknown	Uncertainty: not reported in legacy extract 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 5, ESM-2 / SJC row, AUROC column Source checking is not independent reproduction.
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.
CLAPE-SMB: COACH420, trained on CHEN11 Configuration: CLAPE-SMBProtocol: COACH420, trained on CHEN11 (protein-small molecule binding-site prediction)Dataset: COACH420, trained on CHEN11 Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test. Author-reported evaluation · Evaluation metadata: needs review
0.876 ± 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 2 (Tab2), row 4 CLAPE-SMB, column 5: COACH420, trained on CHEN11 AUROC Source checking is not independent reproduction.
0.395 ± 0.066 Recall Unit: unitless · Direction: higher	Uncertainty: printed: 0.066; value: 0.066; 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 2 (Tab2), row 4 CLAPE-SMB, column 2: COACH420, trained on CHEN11 Recall Source checking is not independent reproduction.
0.371 ± 0.009 MCC Unit: unitless · Direction: higher	Uncertainty: printed: 0.009; value: 0.009; 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 2 (Tab2), row 4 CLAPE-SMB, column 4: COACH420, trained on CHEN11 MCC Source checking is not independent reproduction.
DeepProSite: UniProtSMB test split Configuration: DeepProSiteProtocol: UniProtSMB test split (protein-small molecule binding-site prediction)Dataset: UniProtSMB 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
0.490 ± 0.013 Recall Unit: unitless · Direction: higher	Uncertainty: printed: 0.013; value: 0.013; 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 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall Source checking is not independent reproduction.
CLAPE-SMB: UniProtSMB test split Configuration: CLAPE-SMBProtocol: UniProtSMB test split (protein-small molecule binding-site prediction)Dataset: UniProtSMB 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
0.743 ± 0.040 Precision Unit: unitless · Direction: higher	Uncertainty: printed: 0.040; value: 0.04; 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 4 (Tab4), row 5 CLAPE-SMB, column 3: UniProtSMB test split Precision Source checking is not independent reproduction.
0.673 ± 0.031 Recall Unit: unitless · Direction: higher	Uncertainty: printed: 0.031; value: 0.031; 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 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall Source checking is not independent reproduction.
0.699 ± 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 4 (Tab4), row 5 CLAPE-SMB, column 4: UniProtSMB test split MCC Source checking is not independent reproduction.
GraphBind: UniProtSMB test split Configuration: GraphBindProtocol: UniProtSMB test split (protein-small molecule binding-site prediction)Dataset: UniProtSMB 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
0.932 ± 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 4 (Tab4), row 3 GraphBind, column 5: UniProtSMB test split AUROC Source checking is not independent reproduction.
0.565 ± 0.020 Recall Unit: unitless · Direction: higher	Uncertainty: printed: 0.020; value: 0.02; 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 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall Source checking is not independent reproduction.
P2Rank: COACH420, trained on CHEN11 Configuration: P2RankProtocol: COACH420, trained on CHEN11 (protein-small molecule binding-site prediction)Dataset: COACH420, trained on CHEN11 Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test. Result quoted from another source · Evaluation metadata: needs review
0.079 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 2 (Tab2), row 2 P2Rank, column 3: COACH420, trained on CHEN11 Precision 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 2 (Tab2), row 2 P2Rank, column 5: COACH420, trained on CHEN11 AUROC 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.
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.
GraphBind: COACH420, trained on CHEN11 Configuration: GraphBindProtocol: COACH420, trained on CHEN11 (protein-small molecule binding-site prediction)Dataset: COACH420, trained on CHEN11 Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test. Result quoted from another source · Evaluation metadata: needs review
0.477 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 2 (Tab2), row 3 GraphBind, column 2: COACH420, trained on CHEN11 Recall Source checking is not independent reproduction.
0.889 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 2 (Tab2), row 3 GraphBind, column 5: COACH420, trained on CHEN11 AUROC Source checking is not independent reproduction.
0.303 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 2 (Tab2), row 3 GraphBind, column 4: COACH420, trained on CHEN11 MCC Source checking is not independent reproduction.
0.223 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 2 (Tab2), row 3 GraphBind, column 3: COACH420, trained on CHEN11 Precision Source checking is not independent reproduction.
P2Rank: UniProtSMB test split Configuration: P2RankProtocol: UniProtSMB test split (protein-small molecule binding-site prediction)Dataset: UniProtSMB 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
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 4 (Tab4), row 2 P2Rank, column 5: UniProtSMB test split AUROC Source checking is not independent reproduction.
0.236 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 4 (Tab4), row 2 P2Rank, column 4: UniProtSMB test split MCC 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.

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

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

Table 2; XML table Tab2
Table 3; XML table Tab3
Table 4; XML table Tab4

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

Binding residues are rare and incomplete annotations are discussed in the source. SJC, COACH420 and UniProtSMB results are distinct evaluations, not one shared test set.
Sources
Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages

Profile review details

Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.

Stable record: reported-task-b181ed450cdd41

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.

17 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
Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps ["Input: Protein amino-acid sequences.","Evaluation: Supervised residue-level predictor fitted on the training proteins.","Readout: Precision, recall, MCC, AUROC and AUPRC."] Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Computational evaluation flow Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Datasets SJC combines sc-PDB, JOINED and COACH420; UniProtSMB supplies a separately curated binding-site dataset. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Splits UniProtSMB representative proteins are partitioned 80:10:10 for training, validation and testing. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Adaptation Supervised residue-level predictor fitted on the training proteins. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Metrics Precision, recall, MCC, AUROC and AUPRC. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Baselines ESM-2 versus ProtBert embeddings and MLP/CNN/Transformer head ablations; some head/model comparisons use the test set. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Leakage controls Protein similarity clustering and cluster-aware split comparisons are described; ESM-2 pretraining sequences are not universally excluded. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Uncertainty Multiple random seeds are evaluated; the paper reports fold-averaged metrics and standard deviations for its robustness experiment. Individual claims	Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning Original source ↗ Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `215919244c3dd2dfb0b55fce91c211430fd8d4aee4bb28bd03eab9f4feb73e62` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-09-17-d277315f7d76 · 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
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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Stable ID: reported-task-b181ed450cdd41

areas: proteins-complexes
tasks: protein-small molecule binding-site prediction
entity level: task
version: Not reported
task: protein-small molecule binding-site prediction
scope note: Paper-specific evaluation task; protocol completeness requires further extraction.
comparison panels: id: clape-smb-2024-tab2-recall; title: COACH420, trained on CHEN11 · Recall; protocol id: paper-protocol-efe21a629d215d8f9a; dataset id: paper-dataset-d71026cdf5608821b0; metric: Recall; unit: unitless; direction: higher; result ids: paper-result-cac8b5d6d782329a59; paper-result-519265cd5397a983df; paper-result-8bf20d3347841d493b; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models trained on CHEN11 and tested on COACH420; Table 2 (Tab2), row 2 P2Rank, column 2: COACH420, trained on CHEN11 Recall; Table 2 (Tab2), row 3 GraphBind, column 2: COACH420, trained on CHEN11 Recall; Table 2 (Tab2), row 4 CLAPE-SMB, column 2: COACH420, trained on CHEN11 Recall; context: Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test.; 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-tab2-precision; title: COACH420, trained on CHEN11 · Precision; protocol id: paper-protocol-efe21a629d215d8f9a; dataset id: paper-dataset-d71026cdf5608821b0; metric: Precision; unit: unitless; direction: higher; result ids: paper-result-2b798318eda882028c; paper-result-9000014b7e3080e2bc; paper-result-cef2f0889aade7c724; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models trained on CHEN11 and tested on COACH420; Table 2 (Tab2), row 2 P2Rank, column 3: COACH420, trained on CHEN11 Precision; Table 2 (Tab2), row 3 GraphBind, column 3: COACH420, trained on CHEN11 Precision; Table 2 (Tab2), row 4 CLAPE-SMB, column 3: COACH420, trained on CHEN11 Precision; context: Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test.; 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-tab2-mcc; title: COACH420, trained on CHEN11 · MCC; protocol id: paper-protocol-efe21a629d215d8f9a; dataset id: paper-dataset-d71026cdf5608821b0; metric: MCC; unit: unitless; direction: higher; result ids: paper-result-e198855db4ce0af942; paper-result-7c1331725b140d527d; paper-result-941dc460e719b42566; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models trained on CHEN11 and tested on COACH420; Table 2 (Tab2), row 2 P2Rank, column 4: COACH420, trained on CHEN11 MCC; Table 2 (Tab2), row 3 GraphBind, column 4: COACH420, trained on CHEN11 MCC; Table 2 (Tab2), row 4 CLAPE-SMB, column 4: COACH420, trained on CHEN11 MCC; context: Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test.; 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-tab2-auroc; title: COACH420, trained on CHEN11 · AUROC; protocol id: paper-protocol-efe21a629d215d8f9a; dataset id: paper-dataset-d71026cdf5608821b0; metric: AUROC; unit: unitless; direction: higher; result ids: paper-result-3429737973d4fc729a; paper-result-6dccf13adc1b0316ba; paper-result-061666088fe4993266; source ids: clape-smb-2024; source locator: Comparison of CLAPE-SMB with other models trained on CHEN11 and tested on COACH420; Table 2 (Tab2), row 2 P2Rank, column 5: COACH420, trained on CHEN11 AUROC; Table 2 (Tab2), row 3 GraphBind, column 5: COACH420, trained on CHEN11 AUROC; Table 2 (Tab2), row 4 CLAPE-SMB, column 5: COACH420, trained on CHEN11 AUROC; context: Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test.; 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-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; 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: evidence-expansion-clape-smb-2024-21591924; inspected locators: Table 2; XML table Tab2; Table 3; XML table Tab3; Table 4; XML table Tab4; 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.
historical missing metadata: protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: clape-smb-2024; source locator: Methods: Evaluation metrics; SJC dataset preparation; UniProtSMB dataset preparation; Discussion; cached text lines 24–25, 35–43, 93; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.

Related records

dataset: SJC
benchmark: CLAPE-SMB with ESM-2: protein-small molecule binding-site prediction
evaluates task: SJC test split (protein-small molecule binding-site prediction)
evaluates task: UniProtSMB test split (protein-small molecule binding-site prediction)
evaluates task: COACH420, trained on CHEN11 (protein-small molecule binding-site prediction)

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