Configuration

Boltz-2 (without affinity module), 1 sample, timed per compound

Predicts a protein-ligand complex from sequence and SMILES, producing 1 sample per pair.

Overview

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Evaluations and results

1 evaluation · 6 results. Different protocols are not a single leaderboard.

Protocol: Co-folding time per compound on five DEKOIS 2.0 targets (Shen et al. 2025 Table 5) · Dataset: DEKOIS 2.0 speed subset, five targets with 400 decoys each

Sorted by Runtime (Average total time per compound on one NVIDIA H100 80 GB, averaged over the five targets) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Runtime (Average total time per compound on one NVIDIA H100 80 GB, averaged over the five targets)	Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target a2a)	Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target ar)	Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target cdk2)	Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target ctsk)	Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target hdac2)
Boltz-2 (without affinity module), 1 sample, timed per compoundEvaluation	7.79	10.8	6.14	7.11	6.05	8.79

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Boltz-2 (without affinity module), 1 sample, timed per compound	Protocol: Co-folding time per compound on five DEKOIS 2.0 targets (Shen et al. 2025 Table 5) Dataset: DEKOIS 2.0 speed subset, five targets with 400 decoys each	10.8 Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target a2a) second · lower Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (without affinity module) with 1 sample(s): time per compound (Shen et al. 2025 Table 5) hitdisc-20261022-protocol-shen-speed Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 5, row 'Boltz-2 (without affinity module)' (Number of samples = 1), column 'a2a'
Configuration: Boltz-2 (without affinity module), 1 sample, timed per compound	Protocol: Co-folding time per compound on five DEKOIS 2.0 targets (Shen et al. 2025 Table 5) Dataset: DEKOIS 2.0 speed subset, five targets with 400 decoys each	6.14 Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target ar) second · lower Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (without affinity module) with 1 sample(s): time per compound (Shen et al. 2025 Table 5) hitdisc-20261022-protocol-shen-speed Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 5, row 'Boltz-2 (without affinity module)' (Number of samples = 1), column 'ar'
Configuration: Boltz-2 (without affinity module), 1 sample, timed per compound	Protocol: Co-folding time per compound on five DEKOIS 2.0 targets (Shen et al. 2025 Table 5) Dataset: DEKOIS 2.0 speed subset, five targets with 400 decoys each	7.79 Runtime (Average total time per compound on one NVIDIA H100 80 GB, averaged over the five targets) second · lower Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (without affinity module) with 1 sample(s): time per compound (Shen et al. 2025 Table 5) hitdisc-20261022-protocol-shen-speed Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 5, row 'Boltz-2 (without affinity module)' (Number of samples = 1), column 'Average'
Configuration: Boltz-2 (without affinity module), 1 sample, timed per compound	Protocol: Co-folding time per compound on five DEKOIS 2.0 targets (Shen et al. 2025 Table 5) Dataset: DEKOIS 2.0 speed subset, five targets with 400 decoys each	7.11 Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target cdk2) second · lower Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (without affinity module) with 1 sample(s): time per compound (Shen et al. 2025 Table 5) hitdisc-20261022-protocol-shen-speed Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 5, row 'Boltz-2 (without affinity module)' (Number of samples = 1), column 'cdk2'
Configuration: Boltz-2 (without affinity module), 1 sample, timed per compound	Protocol: Co-folding time per compound on five DEKOIS 2.0 targets (Shen et al. 2025 Table 5) Dataset: DEKOIS 2.0 speed subset, five targets with 400 decoys each	6.05 Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target ctsk) second · lower Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (without affinity module) with 1 sample(s): time per compound (Shen et al. 2025 Table 5) hitdisc-20261022-protocol-shen-speed Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 5, row 'Boltz-2 (without affinity module)' (Number of samples = 1), column 'ctsk'
Configuration: Boltz-2 (without affinity module), 1 sample, timed per compound	Protocol: Co-folding time per compound on five DEKOIS 2.0 targets (Shen et al. 2025 Table 5) Dataset: DEKOIS 2.0 speed subset, five targets with 400 decoys each	8.79 Runtime (Average total time per compound on one NVIDIA H100 80 GB, DEKOIS 2.0 target hdac2) second · lower Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 (without affinity module) with 1 sample(s): time per compound (Shen et al. 2025 Table 5) hitdisc-20261022-protocol-shen-speed Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 5, row 'Boltz-2 (without affinity module)' (Number of samples = 1), column 'hdac2'

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

Shen et al. 2025, Chemical Science (Europe PMC full text) · Original source · PMC12704515 (Chem Sci, published 2025-12-11)

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Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-config-speed-boltz2-no-affinity

areas: molecular-interactions
contexts: research
method types: foundation_model
reported name: Boltz-2 (without affinity module)
configuration type: paper_evaluation
foundation model eligible: true
review: method: scope-review; automated-source-review; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; date: 2026-10-22; method note: Read the record against the pinned sources and against docs/use-cases.md and docs/record-contract.md.; note: Record checked against the pinned source and the record contract. Transcription checked; not reproduced and not reviewed by a human scientist.; artifact sha256: 11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12704515/fullTextXML; receipt: data/omics/use-case-coverage-hitdisc-20261022/review.json
version: Boltz-2 version 2.0.0, the recommended single model with random seed 1, MMseqs2 web-service MSAs, affinity module disabled
samples: 1
hardware: accelerator: NVIDIA H100; memory: 80 GB; count: 1
parameters: Pre-computed MSAs and ligand SMILES as input; all other parameters at default or recommended values
source locator: Table 5 caption; Results 'Assessment of computational efficiency'

Related records

configuration of: Boltz-2
system: Boltz-2 (without affinity module) with 1 sample(s): time per compound (Shen et al. 2025 Table 5)

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