Datasets
No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.
inapplicable
Task
Protein design / inverse folding
Inverse-folding evaluation asks whether a method can propose amino-acid sequences compatible with a specified protein structure.
Sources
dauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentationNo reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.
Overview
Metrics
Protocol-specific sequence recovery or structural assessment; experimental validation, when available, is a separate endpoint.
Allowed inputs
A target protein backbone and declared structural or sequence constraints for an inverse-folding protocol.
Sources
dauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentationEvaluation procedure diagram
How it worksConceptual evaluation workflow
Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.
Sources
dauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentationSource 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
Keep inverse folding separate from sequence-only generation and experimental function. ProteinMPNN takes structural context and produces sequence probabilities or candidate sequences. A concrete benchmark must state the held-out structures, permitted constraints and assessment. Recovery of a reference sequence and experimental success answer different questions.
Sources
dauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentationTask 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
dauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentationRun 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
- A specified structural target provides a clear conditioning context for evaluating sequence proposals.
Sources
dauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation
Limitations and conditions
- Reference-sequence recovery does not by itself establish folding, function or experimental success.
Sources
dauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation
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-designSpecifications
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.Sourcesdauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation |
| Datasets | No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicableSourcesdauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation |
| Organisms | No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicableSourcesdauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation |
| Assays | No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicableSourcesdauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation |
| Splits | No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicableSourcesdauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation |
| Allowed inputs | A target protein backbone and declared structural or sequence constraints for an inverse-folding protocol.Sourcesdauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation |
| Adaptation | No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicableSourcesdauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation |
| Metrics | Protocol-specific sequence recovery or structural assessment; experimental validation, when available, is a separate endpoint.Sourcesdauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation |
| Baselines | Use inverse-folding comparators supplied with the selected benchmark and match structural inputs and constraints.Sourcesdauparas/ProteinMPNN official source · ProteinMPNN README: overview, scoring outputs and training documentation |
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-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Robust deep learning based protein sequence design using ProteinMPNN | PMC primary-source artifact, version pinned by SHA256 | Read source DOI: 10.1126/science.add2187 |
Historical gaps recorded on 2026-09-17
- Protein design is a broad task. ProteinMPNN reports native sequence recovery on 402 backbones and separate noisy-backbone/experimental design evaluations; no general protein-design ranking. New primary paper pinned, concrete protocol extraction required.
Search and extraction details
broad task requires concrete protocol links
Searches
- Protein design / inverse folding primary paper benchmark results
Evidence locations
- Native-backbone test in Results and Figure2A; Methods; Table1
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 | dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
Diagram steps
| dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
| Diagram title Conceptual evaluation workflow Individual claims | dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
| Organisms No shared organism population is defined at this guide level. Record it for each selected dataset. Individual claims | dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
| Assays No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. Individual claims | dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
| Splits No executable split is attached to this task identity. Use the selected protocol’s split manifest. Individual claims | dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
| Allowed inputs A target protein backbone and declared structural or sequence constraints for an inverse-folding protocol. Individual claims | dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
| Adaptation No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. Individual claims | dauparas/ProteinMPNN official source ProteinMPNN README: overview, scoring outputs and training documentation Version: 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57 | 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: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: discovered
3 source records and release history
- ProteinMPNN official resource · Original source · Not reported
- Robust deep learning based protein sequence design using ProteinMPNN · Original source · PMC primary-source artifact, version pinned by SHA256
- dauparas/ProteinMPNN official source · Original source · 8907e6671bfbfc92303b5f79c4b5e6ce47cdef57
Technical metadata and extraction receipts
Stable ID: catalog-task-protein-design
- areas
- proteins-complexes
- entity level
- task
- version
- Not reported
- task
- Protein design / inverse folding
- scope note
- Score or design sequences conditional on a known structure.
- benchmark research
- review date: 2026-09-17; status: broad_task_requires_concrete_protocol_links; primary sources: evidence-expansion-p2-proteinmpnn-original-3e9042dc0ac2; inspected locators: Native-backbone test in Results and Figure2A; Methods; Table1; searched queries: Protein design / inverse folding primary paper benchmark results; gaps: Protein design is a broad task. ProteinMPNN reports native sequence recovery on 402 backbones and separate noisy-backbone/experimental design evaluations; no general protein-design ranking. New primary paper pinned, concrete protocol extraction required.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- 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: src-discovery-dauparas-proteinmpnn; source locator: ProteinMPNN README: overview, scoring outputs and training documentation; ambiguities: None recorded