Datasets
No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.
inapplicable
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.No reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.
Overview
Metrics
Structure-quality measures such as LDDT or TM-score where specified by the protocol; exact residue inclusion and aggregation remain explicit.
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.Evaluation procedure diagram
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.Source reviewed · Automated source review, 2026-09-16. All specifications and missing details
Results
All evaluations
0 evaluations · 0 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
No evaluations linked in this release.
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
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.Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
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-structureSpecifications
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.
| Property | Description and evidence |
|---|---|
| Entity type | Task guide; concrete protocol identities remain separate.SourcesAlphaFold 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 applicableSourcesAlphaFold 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 applicableSourcesAlphaFold 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 applicableSourcesAlphaFold 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 applicableSourcesAlphaFold 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.SourcesAlphaFold 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 applicableSourcesAlphaFold 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.SourcesAlphaFold 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.SourcesAlphaFold 3 paper · AlphaFold 3 Methods: Metrics and recent PDB comparisons. Monomer scope is defined by this catalogue guide. |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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 |
Historical gaps recorded on 2026-09-17
- 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
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
| 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 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 | source checked automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
Diagram steps
| AlphaFold 3 paper 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 | source checked automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Diagram title Conceptual evaluation workflow Individual claims | AlphaFold 3 paper 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 | source checked automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | AlphaFold 3 paper 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 | source checked automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | AlphaFold 3 paper 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 | inapplicable automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Organisms No shared organism population is defined at this guide level. Record it for each selected dataset. Individual claims | AlphaFold 3 paper 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 | inapplicable automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Assays No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. Individual claims | AlphaFold 3 paper 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 | inapplicable automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Splits No executable split is attached to this task identity. Use the selected protocol’s split manifest. Individual claims | AlphaFold 3 paper 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 | inapplicable automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
| 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 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 | source checked automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
| 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 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 | inapplicable automated source review · 2026-09-16 Audit detailsReviewed 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: Source artifact SHA-256: Hash scope: primary_artifact_review |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · 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
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