Task

Monomer structure

Monomer-structure evaluation measures the accuracy of a predicted individual protein structure against a specified reference.

Sources

AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.

0 evaluations · 0 metric rows

At a glance

Inputs, training, access and other details

Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Entity type	Task guide; concrete protocol identities remain separate. Sources AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.
Datasets	No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicable Sources AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.
Organisms	No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicable Sources AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.
Assays	No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicable Sources AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.
Splits	No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicable Sources AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.
Allowed inputs	A protein sequence with any protocol-permitted alignments or templates; an experimental chain structure for reference-based scoring. Sources AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.
Adaptation	No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicable Sources AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.
Metrics	Structure-quality measures such as LDDT or TM-score where specified by the protocol; exact residue inclusion and aggregation remain explicit. Sources AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.
Baselines	Compare structure predictors under declared input information and sampling budgets rather than treating all sequence-to-structure runs as equivalent. Sources AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.

How it works

How it worksConceptual evaluation workflow

Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.

Sources

AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.

Choosing an evaluation

Define whether the method receives only sequence or also evolutionary and template information. Score the individual chain with the chosen alignment and residue-coverage rules. A monomer score is not a protein-interface score, and confidence estimates are not experimental reference measurements.

Sources

AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.

Task scope

This is a task guide, not a single versioned benchmark protocol. The connected resources provide examples or concrete procedures. A candidate method or proposed control is not evidence that an evaluation has been completed.

Sources

AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

No evaluations linked in this release.

Papers and result coverage

Last literature check: 2026-09-17. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.

Paper or primary resource	Version	Reference
proteinbench primary benchmark evidence	2409.06744v1	Read source DOI: 10.48550/arXiv.2409.06744

What is still missing

Mean and median are separate aggregates; slash pairs are not confidence bounds.
ESMFold Science publisher full-text request returned HTTP 403; its DOI was discovered but not used for uninspected full-text claims.

Search and extraction details

broad task primary protocol linked

Searches

Open Problems single cell label projection benchmark v1.0.0 paper
CAPRI assessment rounds 46 54 protein docking results
GEARS predicting transcriptional outcomes multigene perturbations 2023
scVI scANVI reference mapping benchmark primary paper
Boltz-2 affinity benchmark paper
ESMFold monomer structure benchmark Science 2023
"ProkBERT" "paper" "2024"
"scPertEval"
ProkBERT family prokaryotic language models microbe paper
Probabilistic harmonization annotation single-cell transcriptomics scANVI Nature Methods 2021
Evolutionary-scale prediction atomic-level protein structure language model ESMFold Science Lin 2023
Towards Principled Evaluation Single-Cell Perturbation Prediction Models Schäfer 2026

Evidence locations

ProteinBench Section 3.2.1 and Table 7

Strengths and limitations

Strengths supported by sources

Chain-level reference comparison isolates a clearly defined structural endpoint.
Sources
AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.

Limitations and conditions

A correct monomer fold does not establish the arrangement or accuracy of a molecular complex.
Sources
AlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.

Profile review details

Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol.

Stable record: catalog-task-protein-monomer-structure

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

17 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact
Diagram steps ["Fix reference chain and allowed inputs","Predict the monomer structure","Align and match scored residues","Measure declared structural accuracy"] Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact
Diagram title Conceptual evaluation workflow Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact
Entity type Task guide; concrete protocol identities remain separate. Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact
Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact
Organisms No shared organism population is defined at this guide level. Record it for each selected dataset. Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact
Assays No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact
Splits No executable split is attached to this task identity. Use the selected protocol’s split manifest. Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact
Allowed inputs A protein sequence with any protocol-permitted alignments or templates; an experimental chain structure for reference-based scoring. Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact
Adaptation No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. Individual claims	AlphaFold 3 paper Original source ↗ AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 Retrieved: 2026-09-16T19:56:24.856478+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.6.value` Source artifact SHA-256: `e627083f74d990b275e96a7503eee3e3eae9e3035b8efb28321277fcac6f1d6e` Hash scope: primary_artifact_review Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

Release 2026-09-17-d277315f7d76 · Record review: discovered

5 source records and release history

ESM-2 official resource · Original source · Not reported
ESMFold official resource · Original source · Not reported
Chai-1 official resource · Original source · Not reported
proteinbench primary benchmark evidence · Original source · 2409.06744v1
AlphaFold 3 paper · Original source · Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16

Download this release

Technical metadata and extraction receipts

Stable ID: catalog-task-protein-monomer-structure

areas: proteins-complexes
entity level: task
version: Not reported
task: Monomer structure
scope note: Predict single-chain structure from sequence.
benchmark research: review date: 2026-09-17; status: broad_task_primary_protocol_linked; primary sources: expansion-p3-proteinbench; inspected locators: ProteinBench Section 3.2.1 and Table 7; searched queries: Open Problems single cell label projection benchmark v1.0.0 paper; CAPRI assessment rounds 46 54 protein docking results; GEARS predicting transcriptional outcomes multigene perturbations 2023; scVI scANVI reference mapping benchmark primary paper; Boltz-2 affinity benchmark paper; ESMFold monomer structure benchmark Science 2023; "ProkBERT" "paper" "2024"; "scPertEval"; ProkBERT family prokaryotic language models microbe paper; Probabilistic harmonization annotation single-cell transcriptomics scANVI Nature Methods 2021; Evolutionary-scale prediction atomic-level protein structure language model ESMFold Science Lin 2023; Towards Principled Evaluation Single-Cell Perturbation Prediction Models Schäfer 2026; gaps: Mean and median are separate aggregates; slash pairs are not confidence bounds.; ESMFold Science publisher full-text request returned HTTP 403; its DOI was discovered but not used for uninspected full-text claims.; claim scope: Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
historical missing metadata: protocol version: not_yet_extracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: This record identifies the biological prediction question or a suite-specific task, rather than a uniquely fixed evaluated procedure. Preserve its task identity and leave split, model adaptation and scoring details on linked protocols/evaluations.; source ids: evidence-alphafold-paper; source locator: AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide.; ambiguities: None recorded

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