Method

ClusPro rigid-body docking

PIPER sampling, cluster-population ranking and local minimisation as described in the 2020 primary article.

Overview

PIPER sampling, cluster-population ranking and local minimisation as described in the 2020 primary article.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

16 evaluations · 111 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top10 Dataset subset: BM5 Bound antibody Table1 cohort	7 targets_with_acceptable_or_better_model targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, first (top10) row; Good models Number
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top10 Dataset subset: BM5 Bound antibody Table1 cohort	0 acceptable_or_better_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, first (top10) row; difficult column; acceptable_or_better_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top10 Dataset subset: BM5 Bound antibody Table1 cohort	0 high_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, first (top10) row; difficult column; high_accuracy_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top10 Dataset subset: BM5 Bound antibody Table1 cohort	0 medium_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, first (top10) row; difficult column; medium_accuracy_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top10 Dataset subset: BM5 Bound antibody Table1 cohort	7 acceptable_or_better_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, first (top10) row; easy column; acceptable_or_better_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top10 Dataset subset: BM5 Bound antibody Table1 cohort	2 high_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, first (top10) row; easy column; high_accuracy_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top10 Dataset subset: BM5 Bound antibody Table1 cohort	4 medium_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, first (top10) row; easy column; medium_accuracy_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top10 Dataset subset: BM5 Bound antibody Table1 cohort	N/A acceptable_or_better_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, first (top10) row; intermediate column; acceptable_or_better_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top10 Dataset subset: BM5 Bound antibody Table1 cohort	58.3% success_at_10 percent · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, first (top10) row; Good models %
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top30 Dataset subset: BM5 Bound antibody Table1 cohort	10 targets_with_acceptable_or_better_model targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top30 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, second (top30) row; Good models Number
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top30 Dataset subset: BM5 Bound antibody Table1 cohort	0 acceptable_or_better_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top30 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, second (top30) row; difficult column; acceptable_or_better_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top30 Dataset subset: BM5 Bound antibody Table1 cohort	0 high_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top30 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, second (top30) row; difficult column; high_accuracy_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top30 Dataset subset: BM5 Bound antibody Table1 cohort	0 medium_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top30 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, second (top30) row; difficult column; medium_accuracy_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top30 Dataset subset: BM5 Bound antibody Table1 cohort	10 acceptable_or_better_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top30 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, second (top30) row; easy column; acceptable_or_better_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top30 Dataset subset: BM5 Bound antibody Table1 cohort	3 high_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top30 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, second (top30) row; easy column; high_accuracy_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top30 Dataset subset: BM5 Bound antibody Table1 cohort	6 medium_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top30 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, second (top30) row; easy column; medium_accuracy_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top30 Dataset subset: BM5 Bound antibody Table1 cohort	N/A acceptable_or_better_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top30 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, second (top30) row; intermediate column; acceptable_or_better_targets
Configuration: ClusPro BM5 Table1 antibody	Protocol: ClusPro BM5 Bound antibody top30 Dataset subset: BM5 Bound antibody Table1 cohort	83.3% success_at_30 percent · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Bound antibody top30 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Bound antibody, second (top30) row; Good models %
Configuration: ClusPro BM5 Table1 enzyme-balanced	Protocol: ClusPro BM5 Enzyme top10 Dataset subset: BM5 Enzyme Table1 cohort	51 targets_with_acceptable_or_better_model targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Enzyme top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Enzyme, first (top10) row; Good models Number
Configuration: ClusPro BM5 Table1 enzyme-balanced	Protocol: ClusPro BM5 Enzyme top10 Dataset subset: BM5 Enzyme Table1 cohort	3 acceptable_or_better_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Enzyme top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Enzyme, first (top10) row; difficult column; acceptable_or_better_targets
Configuration: ClusPro BM5 Table1 enzyme-balanced	Protocol: ClusPro BM5 Enzyme top10 Dataset subset: BM5 Enzyme Table1 cohort	0 high_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Enzyme top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Enzyme, first (top10) row; difficult column; high_accuracy_targets
Configuration: ClusPro BM5 Table1 enzyme-balanced	Protocol: ClusPro BM5 Enzyme top10 Dataset subset: BM5 Enzyme Table1 cohort	1 medium_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Enzyme top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Enzyme, first (top10) row; difficult column; medium_accuracy_targets
Configuration: ClusPro BM5 Table1 enzyme-balanced	Protocol: ClusPro BM5 Enzyme top10 Dataset subset: BM5 Enzyme Table1 cohort	44 acceptable_or_better_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Enzyme top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Enzyme, first (top10) row; easy column; acceptable_or_better_targets
Configuration: ClusPro BM5 Table1 enzyme-balanced	Protocol: ClusPro BM5 Enzyme top10 Dataset subset: BM5 Enzyme Table1 cohort	2 high_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Enzyme top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Enzyme, first (top10) row; easy column; high_accuracy_targets
Configuration: ClusPro BM5 Table1 enzyme-balanced	Protocol: ClusPro BM5 Enzyme top10 Dataset subset: BM5 Enzyme Table1 cohort	18 medium_accuracy_targets targets · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClusPro Enzyme top10 Not reported Aggregation: Not reported Performance and its limits in rigid body protein-protein docking · Table1 Enzyme, first (top10) row; easy column; medium_accuracy_targets

Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.

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Versions and evaluated configurations

ClusPro BM5 Table1 antibody · variant of
ClusPro BM5 Table1 category-routing · variant of
ClusPro BM5 Table1 enzyme-balanced · variant of
ClusPro BM5 Table1 others · variant of

Strengths, limitations and unresolved questions

Evidence

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Evidence table

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Sources and history

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Release 2026-09-30-e37e3ab1284d · Record review: source checked

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Performance and its limits in rigid body protein-protein docking · Original source · Structure 28(9):1071–1081.e3; 2020; PMC author manuscript NIHMS1608597

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Technical metadata and extraction receipts

Stable ID: ucc-docking-cluspro-bm5-2020-method

areas: proteins-complexes
source locator: STAR Methods: ClusPro Docking Server
review: method: automated_source_review; reviewed at: 2026-09-30T21:50:23.483497+00:00; date: 2026-09-30; reviewer: Codex primary-source table extraction; note: Source transcription only; not execution, human scientific review or independent reproduction.

Related records

variant of: ClusPro BM5 Table1 antibody
variant of: ClusPro BM5 Table1 category-routing
variant of: ClusPro BM5 Table1 enzyme-balanced
variant of: ClusPro BM5 Table1 others

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