Model type
Hosted AlphaFold 3 structure-prediction service.
Service
AlphaFold 3 Server
AlphaFold Server is Google DeepMind’s hosted interface to AlphaFold 3. It predicts molecular complex structures without a local installation and returns confidence estimates. Its service limits, supported inputs and output terms are separate from the downloadable model.
Sources (2)
AlphaFold Server FAQ; AlphaFold Server terms · FAQ: supported molecules, job size, outputs; Terms: OverviewHow it worksAlphaFold Server workflow
Conceptual service workflow. The deployed checkpoint is not pinned by the public FAQ.
Sources
AlphaFold Server FAQ · Input, templates/MSAs, returned predictions and download questionsUnderlying model: AlphaFold 3. Results on this page belong to this service and its evaluated settings.
At a glance
Inputs
Protein, DNA and RNA sequences, supported modifications, ions and ligands. Current FAQ also permits additional ligands by CCD code and custom protein MSAs/templates.
Sources
AlphaFold Server FAQ · Supported molecule types; CCD code; template and MSA questionsOutputs
Five predictions per seed, downloadable structures and confidence JSON; the top-ranked prediction is shown in the interface.
Sources
AlphaFold Server FAQ · How many predictions are returned?; downloaded JSON filesSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Evaluations 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.
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. 2What the server adds
The service handles the input preparation and presents ranked structures and confidence outputs for download. The current FAQ supports custom protein MSAs and templates, as well as ligands specified by CCD code. These options must be recorded when interpreting a result; a server run is not automatically the same configuration as the original paper.
Sources
AlphaFold Server FAQ · What structure templates and MSA are used?; How do I add a ligand using its CCD code?; How many predictions are returned?Service identity and reproducibility
The FAQ states that the server and released AlphaFold 3 use the same weights and equivalent model code. Their genetic-search implementations can nevertheless produce different alignments, so matching weights does not make every run equivalent. The hosted checkpoint digest is not disclosed, and compiler changes can affect exact repeatability. Preserve job inputs, seeds and outputs when citing an evaluation.
Sources
AlphaFold Server FAQ · Why might Multiple Sequence Alignments differ between AlphaFold 3 and AlphaFold Server?; job repeatability and seed questionsStrengths and limitations
Strengths supported by sources
- Provides a hosted route to predictions and downloadable confidence outputs without maintaining the local inference installation.
Sources (2)
AlphaFold Server FAQ; AlphaFold Server terms · Terms: Overview; FAQ: downloaded outputs - Current input controls expose custom protein MSAs and templates, which helps users document those inputs.
Sources
AlphaFold Server FAQ · What structure templates and MSA are used?
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 - Usage quotas and server terms constrain access and downstream reuse; the service is not an unrestricted batch prediction API.
Sources (3)
AlphaFold Server FAQ; AlphaFold Server terms; AlphaFold Server output terms · Daily quota; Terms and Output Terms: use restrictions - A hosted result cannot establish performance for an unspecified local checkpoint or paper evaluation variant.
Sources (2)
AlphaFold Server FAQ; AlphaFold 3 paper · FAQ reproducibility; paper Methods: separate evaluation variants
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. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction.
Stable record: catalog-model-alphafold-3-serverSpecifications
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 |
|---|---|
| Model type | Hosted AlphaFold 3 structure-prediction service.SourcesAlphaFold Server terms · Overview |
| Architecture | A 48-block Pairformer builds token and pair representations; a diffusion module predicts atomic coordinates and separate heads estimate confidence.SourcesAlphaFold 3 paper · Model architecture; Fig. 1d and Fig. 2 |
| Known versions | The FAQ states that the released AlphaFold 3 and server use the same weights and equivalent model code. It does not supply a public digest identifying the hosted checkpoint.SourcesAlphaFold Server FAQ · Why might Multiple Sequence Alignments differ between AlphaFold 3 and AlphaFold Server? |
| Inputs | Protein, DNA and RNA sequences, supported modifications, ions and ligands. Current FAQ also permits additional ligands by CCD code and custom protein MSAs/templates.SourcesAlphaFold Server FAQ · Supported molecule types; CCD code; template and MSA questions |
| Outputs | Five predictions per seed, downloadable structures and confidence JSON; the top-ranked prediction is shown in the interface.SourcesAlphaFold Server FAQ · How many predictions are returned?; downloaded JSON files |
| Training data | Uses AlphaFold 3. The paper describes PDB-based training and distillation; the server FAQ does not provide a separate hosted-checkpoint training inventory.Sources (2)AlphaFold 3 paper; AlphaFold Server FAQ · Paper Methods: Training regime; FAQ: templates and MSA |
| Training cutoff | The paper gives 2021-09-30 for the standard model’s structural training data. The FAQ does not publish a complete dated training manifest for the hosted deployment; its template-search cutoff is a separate input setting.Sources (2)AlphaFold 3 paper; AlphaFold Server FAQ · Paper Methods: Training regime; FAQ: template and MSA settings and comparison with released AlphaFold 3 |
| Context limits | 5,000 tokens per job. Residues, nucleotides and molecular atoms count differently; this is a hosted-service limit.SourcesAlphaFold Server FAQ · What is the maximum job size allowed? |
| Access | Google-account web service for non-commercial use. FAQ reports 30 jobs per day as checked on 2026-09-16; quotas may change.Sources (2)AlphaFold Server FAQ; AlphaFold Server terms · How many jobs can I run?; Terms: Key things to know |
| Code licence | The service is governed by its Terms of Service. Apache-2.0 applies to the separate downloadable inference code, not to ownership or licensing of the hosted service.Sources (2)AlphaFold Server terms; AlphaFold 3 code licence · Terms: Overview; separate implementation LICENSE |
| Weights licence | Hosted use does not supply a weights licence. Downloadable model parameters are a separate offering under their own terms. · Not applicableSources (2)AlphaFold Server terms; AlphaFold 3 weights terms · Service Terms; Model Parameters Terms |
| Output terms | Non-commercial use restrictions apply. Terms prohibit use with automated protein–ligand/peptide interaction prediction systems and training similar structure-prediction models; downstream notices are required.SourcesAlphaFold Server output terms · Use restrictions |
| Parameters | The hosted checkpoint’s total parameter count is not supplied in the inspected FAQ. No number is inferred from the model name. · Not reported in inspected sourcesSourcesAlphaFold Server FAQ · FAQ: model identity and access; no total parameter count |
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.
38 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.entity_level service Individual claims | AlphaFold Server terms Overview; hosted service identity Version: Last modified 2024-05-08; rendered 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsCorrect the original family classification: this record describes the hosted service, not a separate model family. Historical releases retain the original value. Field: Claim: metadata-correction-6ff08f49b3b45f847dd6 Source artifact SHA-256: Hash scope: rendered_primary_page_review |
| Diagram caption Conceptual service workflow. The deployed checkpoint is not pinned by the public FAQ. Individual claims | AlphaFold Server FAQ Input, templates/MSAs, returned predictions and download questions Version: Rendered public FAQ, 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsRead primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction. Field: Source artifact SHA-256: Hash scope: rendered_primary_page_review |
| Diagram steps ["Specify molecules and input settings","Hosted preparation of features","AlphaFold 3 structure prediction","Rank samples and inspect confidence","Download structures and job records"] Individual claims | AlphaFold Server FAQ Input, templates/MSAs, returned predictions and download questions Version: Rendered public FAQ, 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsRead primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction. Field: Source artifact SHA-256: Hash scope: rendered_primary_page_review |
| Diagram title AlphaFold Server workflow Individual claims | AlphaFold Server FAQ Input, templates/MSAs, returned predictions and download questions Version: Rendered public FAQ, 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsRead primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction. Field: Source artifact SHA-256: Hash scope: rendered_primary_page_review |
| Model type Hosted AlphaFold 3 structure-prediction service. Individual claims | AlphaFold Server terms Overview Version: Last modified 2024-05-08; rendered 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsRead primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction. Field: Source artifact SHA-256: Hash scope: rendered_primary_page_review |
| Architecture A 48-block Pairformer builds token and pair representations; a diffusion module predicts atomic coordinates and separate heads estimate confidence. Individual claims | AlphaFold 3 paper Model architecture; Fig. 1d and Fig. 2 Version: Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsRead primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction. Field: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Weights licence Hosted use does not supply a weights licence. Downloadable model parameters are a separate offering under their own terms. Individual claims | AlphaFold Server terms Service Terms; Model Parameters Terms Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Last modified 2024-05-08; rendered 2026-09-16 | inapplicable automated source review · 2026-09-16 Audit detailsRead primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction. Field: Source artifact SHA-256: Hash scope: rendered_primary_page_review |
| Weights licence Hosted use does not supply a weights licence. Downloadable model parameters are a separate offering under their own terms. Individual claims | AlphaFold 3 weights terms Service Terms; Model Parameters Terms Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: c0f97eda2f1f482fd94d3a38bece18c7069b4a5c | inapplicable automated source review · 2026-09-16 Audit detailsRead primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction. Field: Source artifact SHA-256: Hash scope: primary_artifact_review |
| Output terms Non-commercial use restrictions apply. Terms prohibit use with automated protein–ligand/peptide interaction prediction systems and training similar structure-prediction models; downstream notices are required. Individual claims | AlphaFold Server output terms Use restrictions Version: Last modified 2024-05-08; rendered 2026-09-16 | source checked automated source review · 2026-09-16 Audit detailsRead primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction. Field: Source artifact SHA-256: Hash scope: rendered_primary_page_review |
| Parameters The hosted checkpoint’s total parameter count is not supplied in the inspected FAQ. No number is inferred from the model name. Individual claims | AlphaFold Server FAQ FAQ: model identity and access; no total parameter count Version: Rendered public FAQ, 2026-09-16 | unreported automated source review · 2026-09-16 Audit detailsRead primary paper XML, pinned official repository documentation and licences. Reviewed public server FAQ separately. No model run, independent performance replication or human review. A second automated reviewer checked the AlphaFold source claims and service/model distinction; this is not human review or experimental reproduction. Field: Source artifact SHA-256: Hash scope: rendered_primary_page_review |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: discovered
7 source records and release history
- AlphaFold 3 Server official resource · Original source · Not reported
- AlphaFold 3 paper · Original source · Nature 2024; DOI 10.1038/s41586-024-07487-w; XML retrieved 2026-09-16
- AlphaFold Server terms · Original source · Last modified 2024-05-08; rendered 2026-09-16
- AlphaFold Server FAQ · Original source · Rendered public FAQ, 2026-09-16
- AlphaFold 3 code licence · Original source · c0f97eda2f1f482fd94d3a38bece18c7069b4a5c
- AlphaFold 3 weights terms · Original source · c0f97eda2f1f482fd94d3a38bece18c7069b4a5c
- AlphaFold Server output terms · Original source · Last modified 2024-05-08; rendered 2026-09-16
Technical metadata and extraction receipts
Stable ID: catalog-model-alphafold-3-server
- areas
- molecular-interactions
- method types
- foundation model
- entity level
- service
- version
- hosted server
- reported name
- AlphaFold 3 Server
- access
- Manual, non-commercial server access; output terms restrict automated docking combinations.
- method type
- foundation model
- historical missing metadata
- checkpoint revision: not_yet_extracted; training data: not_yet_extracted; licence: 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
- model
- entity classification
- review date: 2026-09-17; rationale: This record represents access through the hosted AlphaFold Server. Its underlying AlphaFold 3 model and locally runnable implementation remain distinct identities.; source ids: evidence-alphafold-paper; evidence-alphafold-server-terms; evidence-alphafold-server-faq; source locator: Model architecture; Fig. 1d and Fig. 2 | Overview | FAQ: supported molecules, job size, outputs; Terms: Overview; ambiguities: None recorded
Related records
- uses model: AlphaFold 3
- subject: AlphaFold 3 Server: entity level
- subject: AlphaFold 3 Server: uses model AlphaFold 3