Datasets
No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.
inapplicable
Task
Biomolecular complex structure
Complex-structure evaluation tests predicted molecular arrangements against experimentally determined structures.
Sources
AlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation setNo reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.
Overview
Metrics
Protocol-specific structure and interface measures, such as LDDT, DockQ or interface LDDT. State the assessed entities and aggregation.
Allowed inputs
Molecular sequences and chemical identities, with templates or alignments only where the protocol permits them; experimental reference structures for scoring.
Sources
AlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation setEvaluation 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 · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation setSource 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
Declare the molecular partners and the input information available to each method. Assess the relevant chains and interfaces as well as the whole complex, using an explicit chain-assignment rule. Templates, alignments and sampling budgets belong to the evaluated configuration. A confidence estimate is not an experimental accuracy measurement.
Sources
AlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation setTask 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 · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation setRun 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
- Interface-specific scoring can reveal errors hidden by an otherwise accurate large component.
Sources
AlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set
Limitations and conditions
- Agreement with one reference structure does not establish dynamics, binding affinity or every possible conformational state.
Sources
AlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set
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-complex-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 · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set |
| Datasets | No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicableSourcesAlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set |
| Organisms | No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicableSourcesAlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set |
| Assays | No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicableSourcesAlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set |
| Splits | No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicableSourcesAlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set |
| Allowed inputs | Molecular sequences and chemical identities, with templates or alignments only where the protocol permits them; experimental reference structures for scoring.SourcesAlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set |
| Adaptation | No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicableSourcesAlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set |
| Metrics | Protocol-specific structure and interface measures, such as LDDT, DockQ or interface LDDT. State the assessed entities and aggregation.SourcesAlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set |
| Baselines | Compare structure predictors with matched partner definitions and input information. Different sampling budgets require separate reporting.SourcesAlphaFold 3 paper · Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set |
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. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Accurate structure prediction of biomolecular interactions with AlphaFold 3 | Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | Read source |
| CASP16 Protein Monomer Structure Prediction Assessment | Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | Read source |
Historical gaps recorded on 2026-09-17
- complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
Search and extraction details
primary protocol reviewed
Searches
- AlphaFold 3 Boltz2 ligand pose benchmark paper 2025
Evidence locations
- AF3 Fig. 1; Extended Data Table 1; CASP16 assessment Results
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 Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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 Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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 Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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 Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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 Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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 Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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 Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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 Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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 Molecular sequences and chemical identities, with templates or alignments only where the protocol permits them; experimental reference structures for scoring. Individual claims | AlphaFold 3 paper Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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 Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set 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
6 source records and release history
- Chai-1 official resource · Original source · Not reported
- Boltz-2 official resource · Original source · Not reported
- AlphaFold 3 Server official resource · Original source · Not reported
- Accurate structure prediction of biomolecular interactions with AlphaFold 3 · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
- CASP16 Protein Monomer Structure Prediction Assessment · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
- 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-complex-structure
- areas
- molecular-interactions
- entity level
- task
- version
- Not reported
- task
- Biomolecular complex structure
- scope note
- Predict joint structure for interacting proteins and other molecules.
- benchmark research
- review date: 2026-09-17; status: primary_protocol_reviewed; primary sources: evidence-expansion-alphafold3-e627083f; evidence-expansion-casp16-32ef3bdf; inspected locators: AF3 Fig. 1; Extended Data Table 1; CASP16 assessment Results; searched queries: AlphaFold 3 Boltz2 ligand pose benchmark paper 2025; gaps: complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
- 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: Main text: Model architecture and Model limitations; Methods: Metrics and Recent PDB evaluation set; ambiguities: None recorded