Task

Small-molecule affinity

Affinity evaluation tests predictions of molecular binding measurements or binder labels, depending on the protocol.

Sources (2)

jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs

No reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.

0 evaluations · 0 results

Overview

Datasets

No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.

inapplicable

Metrics

Use endpoint-appropriate regression or classification metrics. Do not merge differently transformed affinity quantities into one table without documenting conversions.

Allowed inputs

A protein–small-molecule pair plus any permitted structural information; matched experimental measurements or declared binary labels.

Sources (2)

jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs

Evaluation procedure diagram

How it worksConceptual evaluation workflow

Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.

Sources (2)

jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs

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 the endpoint before comparing numbers. Boltz-2 distinguishes a binder-versus-decoy probability from a quantitative affinity output, with different supervision. Preserve measurement units, transforms and assay conditions. Structural plausibility alone does not validate affinity; a structural dataset also needs checked affinity labels before it can support this task.

Sources (2)

jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs

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 (2)

jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs

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

Separating binding classification from quantitative affinity avoids conflating two different uses of a model output.
Sources (2)
jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs

Limitations and conditions

The inspected PLINDER revision flags its affinity query as disabled after a parsing bug. A dataset name alone does not verify an affinity label.
Sources (2)
jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs

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-ligand-affinity

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.

Data, procedure and scoring
Property	Description and evidence
Entity type	Task guide; concrete protocol identities remain separate. Sources (2) jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs
Datasets	No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicable Sources (2) jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs
Organisms	No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicable Sources (2) jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs
Assays	No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicable Sources (2) jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs
Splits	No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicable Sources (2) jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs
Allowed inputs	A protein–small-molecule pair plus any permitted structural information; matched experimental measurements or declared binary labels. Sources (2) jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs
Adaptation	No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicable Sources (2) jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs
Metrics	Use endpoint-appropriate regression or classification metrics. Do not merge differently transformed affinity quantities into one table without documenting conversions. Sources (2) jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs
Baselines	Select comparators evaluated on the same measured endpoint and split; a docking score is not automatically a calibrated affinity measurement. Sources (2) jwohlwend/boltz: docs/prediction.md; plinder-org/plinder official source · Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs

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
Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction	PMC full-text XML snapshot PMC12262699 at retrieval; byte-pinned by SHA-256	Read source DOI: 10.1101/2025.06.14.659707

Historical gaps recorded on 2026-09-17

Binding probability, mixed-measure affinity regression and virtual-screening enrichment are different outcomes.
Affinity head mixes biochemical quantities; values are not automatically assay-calibrated Kd.
No paper-wide universal affinity score or common ligand denominator.

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

Affinity module
Evaluation
Affinity evaluation figures 12–14

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.

34 evidence rows 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
Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims	jwohlwend/boltz: docs/prediction.md Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc Retrieved: 2026-09-16T19:46:19.465940+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `b9cb2ff437389864bde02e7e9fd9fbcc7de189ca2e240a5f3fb6261ca595a795` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims	plinder-org/plinder official source Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85b3f1cb1763530a6cfd934f4263a1777c41afa4 Retrieved: 2026-09-16T10:30:23.659162+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `1d53c3b89030dc4651d3e7bf4749256b7e579330fc7a660cffaa992d646da34a` Hash scope: Hash scope not separately documented; inspect source record
Diagram steps Fix assay endpoint, units and split Specify model inputs Predict the declared affinity quantity Score matched measurements or labels Individual claims	jwohlwend/boltz: docs/prediction.md Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc Retrieved: 2026-09-16T19:46:19.465940+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `b9cb2ff437389864bde02e7e9fd9fbcc7de189ca2e240a5f3fb6261ca595a795` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps Fix assay endpoint, units and split Specify model inputs Predict the declared affinity quantity Score matched measurements or labels Individual claims	plinder-org/plinder official source Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85b3f1cb1763530a6cfd934f4263a1777c41afa4 Retrieved: 2026-09-16T10:30:23.659162+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `1d53c3b89030dc4651d3e7bf4749256b7e579330fc7a660cffaa992d646da34a` Hash scope: Hash scope not separately documented; inspect source record
Diagram title Conceptual evaluation workflow Individual claims	jwohlwend/boltz: docs/prediction.md Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc Retrieved: 2026-09-16T19:46:19.465940+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `b9cb2ff437389864bde02e7e9fd9fbcc7de189ca2e240a5f3fb6261ca595a795` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title Conceptual evaluation workflow Individual claims	plinder-org/plinder official source Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85b3f1cb1763530a6cfd934f4263a1777c41afa4 Retrieved: 2026-09-16T10:30:23.659162+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `1d53c3b89030dc4651d3e7bf4749256b7e579330fc7a660cffaa992d646da34a` Hash scope: Hash scope not separately documented; inspect source record
Entity type Task guide; concrete protocol identities remain separate. Individual claims	jwohlwend/boltz: docs/prediction.md Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc Retrieved: 2026-09-16T19:46:19.465940+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `b9cb2ff437389864bde02e7e9fd9fbcc7de189ca2e240a5f3fb6261ca595a795` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Entity type Task guide; concrete protocol identities remain separate. Individual claims	plinder-org/plinder official source Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85b3f1cb1763530a6cfd934f4263a1777c41afa4 Retrieved: 2026-09-16T10:30:23.659162+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `1d53c3b89030dc4651d3e7bf4749256b7e579330fc7a660cffaa992d646da34a` 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	jwohlwend/boltz: docs/prediction.md Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc Retrieved: 2026-09-16T19:46:19.465940+00:00	inapplicable automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `b9cb2ff437389864bde02e7e9fd9fbcc7de189ca2e240a5f3fb6261ca595a795` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims	plinder-org/plinder official source Original source ↗ Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85b3f1cb1763530a6cfd934f4263a1777c41afa4 Retrieved: 2026-09-16T10:30:23.659162+00:00	inapplicable automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `1d53c3b89030dc4651d3e7bf4749256b7e579330fc7a660cffaa992d646da34a` Hash scope: Hash scope not separately documented; inspect source record

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

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

4 source records and release history

Boltz-2 official resource · Original source · Not reported
Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction · Original source · PMC full-text XML snapshot PMC12262699 at retrieval; byte-pinned by SHA-256
jwohlwend/boltz: docs/prediction.md · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
plinder-org/plinder official source · Original source · 85b3f1cb1763530a6cfd934f4263a1777c41afa4

Download this release

Technical metadata and extraction receipts

Stable ID: catalog-task-ligand-affinity

areas: molecular-interactions
entity level: task
version: Not reported
task: Small-molecule affinity
scope note: Predict measured binding affinity; pose confidence is not an affinity value.
benchmark research: review date: 2026-09-17; status: broad_task_primary_protocol_linked; primary sources: expansion-p3-boltz2; inspected locators: Affinity module; Evaluation; Affinity evaluation figures 12–14; 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: Binding probability, mixed-measure affinity regression and virtual-screening enrichment are different outcomes.; Affinity head mixes biochemical quantities; values are not automatically assay-calibrated Kd.; No paper-wide universal affinity score or common ligand denominator.; 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-official-5a9e55abdf288d9dd8da; src-discovery-plinder-org-plinder; source locator: Boltz docs/prediction.md: Properties (affinity), Affinity prediction outputs; PLINDER README: Known bugs; ambiguities: None recorded

Related records

Suggest a correction