Configuration

Rosetta scoring function (RSR configuration unresolved)

Rosetta scoring function used by ATOM3D as the state-of-the-art RSR comparison. The specific score function and settings are not stated.

Identified as Rosetta scoring function. The source table prints [Watkins et al., 2020].

App. F.8 states that ATOM3D compares its RSR results 'against the Rosetta scoring function [Alford et al., 2017]', and Tables 7 and 8 give the same values under [Alford et al., 2017]. Table 6 instead cites [Watkins et al., 2020] (FARFAR2). Both citations are Rosetta-based, so the generic identity is supported; the specific scoring function is not.

Comparison: ATOM3D describes the Rosetta scoring function as a physical- and knowledge-based potential tuned for biomolecular structure, which has most consistently produced the lowest-RMSD candidates in past RNA Puzzles.

Not established: Citation conflict. Table 6 cites [Watkins et al., 2020]; Tables 7 and 8 and App. F.8 cite [Alford et al., 2017]. The paper does not explain the difference. Score function and settings. The specific Rosetta score function, weights and software version behind the values are not stated. FARFAR2 is not inferred as the ranking method.

ATOM3D: Tasks On Molecules in Three Dimensions · ATOM3D arXiv:2012.04035v4 Table 6, p.8 ([Watkins et al., 2020]); App. F.8, p.25; Table 7, p.27 and Table 8 RSR rows, p.28 ([Alford et al., 2017]).. AI-assisted source review on 2026-09-24; no human scientific review.

2 evaluations · 2 results

Overview

Rosetta scoring function used by ATOM3D as the state-of-the-art RSR comparison. The specific score function and settings are not stated.

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

Evaluations and results

2 evaluations · 2 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Rosetta scoring function (RSR configuration unresolved) (cited as [Watkins et al., 2020])	Task: ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman Dataset subset: ATOM3D RSR (ATOM3D split)	0.304 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Rosetta scoring function (RSR configuration unresolved) on ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(glob. RS), column([Watkins et al., 2020])
Configuration: Rosetta scoring function (RSR configuration unresolved) (cited as [Watkins et al., 2020])	Task: ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target Dataset subset: ATOM3D RSR (ATOM3D split)	0.173 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Rosetta scoring function (RSR configuration unresolved) on ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(RSR mean RS), column([Watkins et al., 2020])

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ATOM3D: Tasks On Molecules in Three Dimensions · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256

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Technical metadata and extraction receipts

Stable ID: atom3d-method-watkins-et-al-2020

areas: molecular-interactions
source locator: Table 6, column([Watkins et al., 2020])
missing metadata: checkpoint revision: unreported; parameters: unextracted
source label: [Watkins et al., 2020]
source identity: status: resolved; label form: bracketed_citation; display name: Rosetta scoring function (RSR configuration unresolved); identity: Rosetta scoring function; configuration: Not reported; basis: App. F.8 states that ATOM3D compares its RSR results 'against the Rosetta scoring function [Alford et al., 2017]', and Tables 7 and 8 give the same values under [Alford et al., 2017]. Table 6 instead cites [Watkins et al., 2020] (FARFAR2). Both citations are Rosetta-based, so the generic identity is supported; the specific scoring function is not.; source ids: evidence-expansion-atom3d-92656c20; source locator: ATOM3D arXiv:2012.04035v4 Table 6, p.8 ([Watkins et al., 2020]); App. F.8, p.25; Table 7, p.27 and Table 8 RSR rows, p.28 ([Alford et al., 2017]).; known details: label: Comparison; value: ATOM3D describes the Rosetta scoring function as a physical- and knowledge-based potential tuned for biomolecular structure, which has most consistently produced the lowest-RMSD candidates in past RNA Puzzles.; source ids: evidence-expansion-atom3d-92656c20; source locator: ATOM3D App. F.8, p.25; unknown: label: Citation conflict; note: Table 6 cites [Watkins et al., 2020]; Tables 7 and 8 and App. F.8 cite [Alford et al., 2017]. The paper does not explain the difference.; label: Score function and settings; note: The specific Rosetta score function, weights and software version behind the values are not stated. FARFAR2 is not inferred as the ranking method.; original name: [Watkins et al., 2020]; original description: Published state-of-the-art structure ranking method that the ATOM3D authors compare against, named only by its citation in the table.; review: method: automated_source_review; date: 2026-09-24; note: AI-assisted review against the cited primary sources. No human scientific review. Values, locators and comparison conditions are unchanged.

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