Method

ClusPro rigid-body docking

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

Overview

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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

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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 CAPRI acceptable targets (all targets) count · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI high-quality targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI medium targets (difficult (flexible) targets; top 10 models; medium (**) as printed, overlap with high not stated) count · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI high-quality targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI medium targets (easy (rigid-body) targets; top 10 models; medium (**) as printed, overlap with high not stated) count · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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% CAPRI top-10 success rate percent · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (all targets) count · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI high-quality targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI medium targets (difficult (flexible) targets; top 30 models; medium (**) as printed, overlap with high not stated) count · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI high-quality targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI medium targets (easy (rigid-body) targets; top 30 models; medium (**) as printed, overlap with high not stated) count · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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% CAPRI top-30 success rate percent · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (all targets) count · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI high-quality targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI medium targets (difficult (flexible) targets; top 10 models; medium (**) as printed, overlap with high not stated) count · higher Uncertainty: Not reported by the source 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 CAPRI acceptable targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI high-quality targets (by difficulty category) count · higher Uncertainty: Not reported by the source 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 CAPRI medium targets (easy (rigid-body) targets; top 10 models; medium (**) as printed, overlap with high not stated) count · higher Uncertainty: Not reported by the source 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 2026-11-02-a7f03c9e55a5.

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Versions and evaluated configurations

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

Evidence

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Release 2026-11-02-a7f03c9e55a5 · 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; reviewer: codex; note: Source transcription only; not execution, human scientific review or independent reproduction.; reviewer note: role: primary-source table extraction

Related records

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

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