Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
COACH420, trained on CHEN11 (protein-small molecule binding-site prediction)
COACH420, trained on CHEN11 · Recall. Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test.
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 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 RecallAt a glance
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.
| 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. |
How it works
Evaluation in this paper
Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test.
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 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 RecallEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
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.
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.
- 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 RecallValues, uncertainty and evidence
| 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 · 3 evaluations · 12 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| 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. |
| 0.412 ± 0.057 Precision Unit: unitless · Direction: higher | Uncertainty: printed: 0.057; value: 0.057; 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 3: COACH420, trained on CHEN11 Precision 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. |
| 0.888 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 2 P2Rank, column 2: COACH420, trained on CHEN11 Recall Source checking is not independent reproduction. |
| 0.224 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 2 P2Rank, column 4: COACH420, trained on CHEN11 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. |
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 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
Strengths and limitations
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-efe21a629d215d8f9aEvidence 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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test. Individual claims | 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 Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Introduction COACH420, trained on CHEN11 · Recall. Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test. Individual claims | 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 Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 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 Version: version of record | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-b90fb60c354bd2d84a Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
1 source records and release history
- Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning · Original source · version of record
Technical metadata and extraction receipts
Stable ID: paper-protocol-efe21a629d215d8f9a
- areas
- proteins-complexes
- tasks
- protein-small molecule binding-site prediction
- entity level
- protocol
- protocol
- Residue-level small-molecule binding-site classification. CHEN11 training, COACH420 test.
- 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
- 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 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; 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 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; ambiguities: None recorded
Related records
- evaluates task: protein-small molecule binding-site prediction
- subject: COACH420, trained on CHEN11 (protein-small molecule binding-site prediction): links:evaluates_task:reported-task-b181ed450cdd41
- benchmark: P2Rank: COACH420, trained on CHEN11
- benchmark: GraphBind: COACH420, trained on CHEN11
- benchmark: CLAPE-SMB: COACH420, trained on CHEN11