Configuration

AF3

AlphaFold 3 predicts three-dimensional structures of complexes containing proteins, nucleic acids and other molecular components. It combines a Pairformer representation network with an atomic-coordinate diffusion model. This entry describes the model and local implementation; the hosted AlphaFold Server has a separate profile.

Sources (2)

AlphaFold 3 paper; AlphaFold 3 README · Abstract; Model architecture; README: Installation and Usage

1 evaluation · 5 results

How it worksAlphaFold 3 architecture

Conceptual architecture based on the paper. Exact preprocessing and sampling settings belong to each evaluation.

Sources

AlphaFold 3 paper · Fig. 1d; Fig. 2; Model architecture

Overview

Model type

Pairformer plus diffusion model for joint biomolecular structure prediction.

Sources

AlphaFold 3 paper · Model architecture; Fig. 1

Inputs

Protein, DNA and RNA sequences; chemical components; optional MSAs and structural templates.

Sources

AlphaFold 3 input specification · Top-level structure; protein, RNA, DNA and ligand inputs

Outputs

Predicted structures in mmCIF plus confidence outputs, including pLDDT, PAE, pTM and ipTM.

Sources

AlphaFold 3 output specification · Output directory structure; confidence outputs

Access

Public inference implementation; weights downloaded directly from Google under separate non-commercial terms.

Sources

AlphaFold 3 README · Obtaining Model Parameters; Installation and Usage

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

1 evaluation · 5 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AF3	Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95	0.19 angle_rmsd degree · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: unreported in Table 1 footnote Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column angle_rmsd; footnote a
Configuration: AF3	Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95	0.998 ligand_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column ligand_rmsd; footnote a
Configuration: AF3	Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95	70.8% chirality percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: percentage of molecules with consistent chirality Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column chirality; footnote a
Configuration: AF3	Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95	0.363 protein_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a
Configuration: AF3	Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95	0.0192 bond_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column bond_rmsd; footnote a

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

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How it works, versions and access

Related profile: AlphaFold 3. This page retains the exact record and its evaluation context.

This configuration

Exact source-reported configuration or submission label. Family membership, checkpoint identity and aliases have not been inferred.

record: AF3
configuration: Not reported
entity type: Configuration

How it works

Joint structure prediction

Sequence, chemical and evolutionary features feed a Pairformer, which builds representations of individual tokens and their relationships. A diffusion module then predicts atomic coordinates. Separate heads estimate confidence. The paper describes 48 Pairformer blocks; the architecture models complexes jointly rather than treating every partner as a separately folded structure.

Sources

AlphaFold 3 paper · Main text: Model architecture; Fig. 1d and Fig. 2

Training and evaluation context

The standard model uses a structural training cutoff of 30 September 2021. The dedicated PoseBusters Methods section reports a separate model with a 30 September 2019 cutoff, although other training passages disagree (see limitations). Model seeds, templates, input information and ranking also affect the reported comparison; paper evaluation variants are not automatically identical to current downloadable weights.

Sources (2)

AlphaFold 3 paper; AlphaFold 3 supplementary information · Main paper Methods: Training regime, Inference regime and PoseBusters; supplement Section 5.2

Local access

The pinned repository provides inference code and a direct Google-hosted weights download. Its README is more current on access than the server FAQ, which still describes an application form. Code and model parameters have different licences; the server output terms should not be substituted for the local weights terms.

Sources (4)

AlphaFold 3 README; AlphaFold 3 code licence; AlphaFold 3 weights terms; AlphaFold Server FAQ · README: Obtaining Model Parameters and Licences; LICENSE; weights terms: Key things to know; FAQ: model access

Training data and provenance

Training combines experimental PDB structures with approximately 41 million predicted protein monomers, about 25,000 disorder-focused protein complexes and about 65,000 predicted RNA structures. The supplement also lists transcription-factor examples used during fine-tuning. Its sequence-search resources include UniRef90, UniProt, BFD/Uniclust30, MGnify, Rfam and RNAcentral. These resources have different versions and dates: the structural training cutoff is not a cutoff for every sequence database.

Sources

AlphaFold 3 supplementary information · Sections 2.2 and 2.5; Table 3; Section 2.5.2 distillation datasets (PDF pages 8–9, printed pages 3–4)

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths supported by sources

One architecture handles several molecular component types and their joint structures. This is a capability description, not evidence that every complex will be accurate.
Sources
AlphaFold 3 paper · Abstract; Model architecture
The local implementation exposes input, template and output specifications, allowing an evaluation configuration to be documented.
Sources
AlphaFold 3 input specification · Input format and optional input fields

Limitations and conditions

Predictions can contain incorrect chirality, atomic clashes or spurious structure in disordered regions. Confidence and structural plausibility need separate inspection.
Sources
AlphaFold 3 paper · Model limitations; Fig. 5
Sampled structures are not a calibrated solution-state ensemble. Prediction confidence does not establish binding affinity or experimental function.
Sources
AlphaFold 3 paper · Model limitations: dynamics and conformational states; confidence outputs are structure-quality estimates
The public code licence does not remove the separate non-commercial restrictions on weights and outputs.
Sources
AlphaFold 3 weights terms · Key things to know
The source is internally inconsistent about the PoseBusters training cutoff. Its dedicated PoseBusters Methods section and Results specify 2019-09-30, while the general Training regime and supplement Section 5.2 say 2021-09-30. The separate evaluation variant is retained; this profile does not resolve the discrepancy or assign its result to a current downloadable checkpoint.
Sources (2)
AlphaFold 3 paper; AlphaFold 3 supplementary information · Main paper Results and Methods: PoseBusters versus Training regime; supplement Section 5.2, printed page 29

Profile review details

Read primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. Supplementary PDF reviewed, including visual checks of Tables 3 and 6. Conflicting cutoff statements remain explicit. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction.

Stable record: discovery-model-alphafold-3

Specifications

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.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Pairformer plus diffusion model for joint biomolecular structure prediction. Sources AlphaFold 3 paper · Model architecture; Fig. 1
Architecture	A 48-block Pairformer builds token and pair representations; a diffusion module predicts atomic coordinates and separate heads estimate confidence. Sources AlphaFold 3 paper · Model architecture; Fig. 1d and Fig. 2
Known versions	AlphaFold 3; inference code/documentation reviewed at commit c0f97eda2f1f482fd94d3a38bece18c7069b4a5c. This is a software revision, not a weight-file checksum. Paper evaluation variants are distinct configurations. Sources (2) AlphaFold 3 README; AlphaFold 3 paper · Pinned repository revision; paper evaluation distinctions described in Methods
Inputs	Protein, DNA and RNA sequences; chemical components; optional MSAs and structural templates. Sources AlphaFold 3 input specification · Top-level structure; protein, RNA, DNA and ligand inputs
Outputs	Predicted structures in mmCIF plus confidence outputs, including pLDDT, PAE, pTM and ipTM. Sources AlphaFold 3 output specification · Output directory structure; confidence outputs
Training cutoff	Experimental PDB structures plus protein and RNA distillation sets. The standard structural cutoff is 2021-09-30. The dedicated PoseBusters Methods section specifies a separate 2019-09-30 model; other training passages conflict with that date (see below). Sources (2) AlphaFold 3 paper; AlphaFold 3 supplementary information · Main paper Methods: Training regime and PoseBusters; Supplement Sections 2.5 and 5.2
Training data	Experimental PDB structures, protein and RNA distillation sets, and transcription-factor examples used during fine-tuning. Sequence-search databases are separately versioned input resources. Sources AlphaFold 3 supplementary information · Sections 2.2 and 2.5; Table 3; training-data discussion below
Context limits	The default largest compilation bucket is 5,120 tokens. The documentation supports larger inputs by configuration, subject to memory; this is not a universal architectural context limit. Sources AlphaFold 3 performance documentation · Compilation buckets; predicting structures with more than 5,120 tokens
Access	Public inference implementation; weights downloaded directly from Google under separate non-commercial terms. Sources AlphaFold 3 README · Obtaining Model Parameters; Installation and Usage
Code licence	Apache License 2.0. Sources AlphaFold 3 code licence · LICENSE
Weights licence	Custom AlphaFold 3 Model Parameters Terms of Use, last modified 2024-11-09. Non-commercial use by or for non-commercial organisations; additional output and redistribution restrictions apply. Sources AlphaFold 3 weights terms · Key things to know; Use restrictions
Parameters	No total trainable-parameter count is reported in the inspected main paper, supplementary architecture/training sections or implementation documentation. Layer dimensions do not establish a complete checkpoint total. · Not reported in inspected sources Sources (2) AlphaFold 3 paper; AlphaFold 3 supplementary information · Main paper Model architecture; supplement Sections 3–5 and full-text parameter search; implementation documentation

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Relationship: family discovery-model-alphafold-3 Individual claims	Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Original source ↗ Molecular Structure Prediction; Table 1 AF3 row; Figure 2 caption Version: version of record Retrieved: 2026-09-16T10:41:16.555674+00:00	source checked automated source review · 2026-09-23 Audit details Source review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. The source explicitly expands AF3 as AlphaFold3 and states default input parameters. This is not AlphaFold2. Field: `links:family:discovery-model-alphafold-3` Claim: model-evaluation-identity-09c51c303fc50989257d Source artifact SHA-256: `78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: discovered

1 source records and release history

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Original source · version of record

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Technical metadata and extraction receipts

Stable ID: acquired-configuration-359fd4eb92fb3f85c4a5

source locator: Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a
reported configuration: AF3
reference kind: not_a_reference
missing metadata: checkpoint revision: unreported; model family: unextracted

Related records

family: AlphaFold 3
model: AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95
subject: AF3: family AlphaFold 3

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