Configuration

Boltz-2 (AlphaBind pairwise evaluation)

Configuration of Boltz-2: Boltz-2 interface pLDDT (ipLDDT) used as the binding score for each antibody-antigen complex.

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Evaluations and results

4 evaluations · 4 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (pairwise: stronger binder identified within sampled antibody pairs) (higher 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	Protocol and dataset	Accuracy (pairwise: stronger binder identified within sampled antibody pairs)
Boltz-2 (AlphaBind pairwise evaluation)Evaluation	AlphaBind TRA held-out antigen, pairwise accuracy, AlphaBind TRA antibody variants (held-out antigen)	60.1% (best in column)
Boltz-2 (AlphaBind pairwise evaluation)Evaluation	AlphaBind PEM held-out antigen, pairwise accuracy, AlphaBind PEM antibody variants (held-out antigen)	57.9%
Boltz-2 (AlphaBind pairwise evaluation)Evaluation	AlphaBind VHH72 held-out antigen, pairwise accuracy, AlphaBind VHH72 antibody variants (held-out antigen)	57.9%
Boltz-2 (AlphaBind pairwise evaluation)Evaluation	AlphaBind PP489 held-out antigen, pairwise accuracy, AlphaBind PP489 antibody variants (held-out antigen)	55.5%

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Boltz-2 (AlphaBind pairwise evaluation)	Protocol: AlphaBind PEM held-out antigen, pairwise accuracy Dataset: AlphaBind PEM antibody variants (held-out antigen)	57.9% Accuracy (pairwise: stronger binder identified within sampled antibody pairs) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The Table 2 footnote says "Values denote chi-squared statistics, with significance levels in parentheses", which contradicts the column headers ("Pairwise accuracy (%)", "Graphinity (%)" and so on), the cell contents (percentages between 47.11 and 74.27) and the body text, which places the chi-squared statistics in Table S1. The records read the cells as accuracies with a p-value, which the headers and body support; the footnote is wrong as printed.A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation · Table 2 footnote Methods, coverage and source Boltz-2 on AlphaBind PEM (pairwise accuracy) lit-interactions-20261011-mochibind-protocol-alphabind-pem-pairwise-accuracy Aggregation: Not reported A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation · Table 2, row 'PEM', column 'Boltz-2 - iplddt (%)'; STAR Methods, 'Cross-antigen evaluation setup'
Configuration: Boltz-2 (AlphaBind pairwise evaluation)	Protocol: AlphaBind PP489 held-out antigen, pairwise accuracy Dataset: AlphaBind PP489 antibody variants (held-out antigen)	55.5% Accuracy (pairwise: stronger binder identified within sampled antibody pairs) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The Table 2 footnote says "Values denote chi-squared statistics, with significance levels in parentheses", which contradicts the column headers ("Pairwise accuracy (%)", "Graphinity (%)" and so on), the cell contents (percentages between 47.11 and 74.27) and the body text, which places the chi-squared statistics in Table S1. The records read the cells as accuracies with a p-value, which the headers and body support; the footnote is wrong as printed.A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation · Table 2 footnote Methods, coverage and source Boltz-2 on AlphaBind PP489 (pairwise accuracy) lit-interactions-20261011-mochibind-protocol-alphabind-pp489-pairwise-accuracy Aggregation: Not reported A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation · Table 2, row 'PP489', column 'Boltz-2 - iplddt (%)'; STAR Methods, 'Cross-antigen evaluation setup'
Configuration: Boltz-2 (AlphaBind pairwise evaluation)	Protocol: AlphaBind TRA held-out antigen, pairwise accuracy Dataset: AlphaBind TRA antibody variants (held-out antigen)	60.1% Accuracy (pairwise: stronger binder identified within sampled antibody pairs) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The Table 2 footnote says "Values denote chi-squared statistics, with significance levels in parentheses", which contradicts the column headers ("Pairwise accuracy (%)", "Graphinity (%)" and so on), the cell contents (percentages between 47.11 and 74.27) and the body text, which places the chi-squared statistics in Table S1. The records read the cells as accuracies with a p-value, which the headers and body support; the footnote is wrong as printed.A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation · Table 2 footnote Methods, coverage and source Boltz-2 on AlphaBind TRA (pairwise accuracy) lit-interactions-20261011-mochibind-protocol-alphabind-tra-pairwise-accuracy Aggregation: Not reported A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation · Table 2, row 'TRA', column 'Boltz-2 - iplddt (%)'; STAR Methods, 'Cross-antigen evaluation setup'
Configuration: Boltz-2 (AlphaBind pairwise evaluation)	Protocol: AlphaBind VHH72 held-out antigen, pairwise accuracy Dataset: AlphaBind VHH72 antibody variants (held-out antigen)	57.9% Accuracy (pairwise: stronger binder identified within sampled antibody pairs) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The Table 2 footnote says "Values denote chi-squared statistics, with significance levels in parentheses", which contradicts the column headers ("Pairwise accuracy (%)", "Graphinity (%)" and so on), the cell contents (percentages between 47.11 and 74.27) and the body text, which places the chi-squared statistics in Table S1. The records read the cells as accuracies with a p-value, which the headers and body support; the footnote is wrong as printed.A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation · Table 2 footnote Methods, coverage and source Boltz-2 on AlphaBind VHH72 (pairwise accuracy) lit-interactions-20261011-mochibind-protocol-alphabind-vhh72-pairwise-accuracy Aggregation: Not reported A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation · Table 2, row 'VHH72', column 'Boltz-2 - iplddt (%)'; STAR Methods, 'Cross-antigen evaluation setup'

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A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation · Original source · iScience 2026, 116522; PMC13444443 full-text XML

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Technical metadata and extraction receipts

Stable ID: lit-interactions-20261011-mochibind-config-boltz-2-alphabind-pairwise

areas: molecular-interactions; proteins-complexes
contexts: research
method types: foundation_model
reported name: Boltz-2 - iplddt
foundation model eligible: true
parameters: Boltz-2 interface pLDDT (ipLDDT) used as the binding score for each antibody-antigen complex
source locator: Table 2 header and note; STAR Methods
access reuse: Not stated in the source
missing metadata: version: reason: unreported; note: No checkpoint version printed
provenance note: Boltz-2 as evaluated on AlphaBind pairwise accuracy in the MochiBind study.

Related records

configuration of: Boltz-2
system: Boltz-2 on AlphaBind PEM (pairwise accuracy)
system: Boltz-2 on AlphaBind PP489 (pairwise accuracy)
system: Boltz-2 on AlphaBind TRA (pairwise accuracy)
system: Boltz-2 on AlphaBind VHH72 (pairwise accuracy)

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