Task

Protein–ligand pose

Protein–ligand pose evaluation checks both agreement with a reference pose and the plausibility of the predicted geometry.

Sources (2)

maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions

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

Reference-pose error and explicitly versioned plausibility checks. A validity pass without a matching pose is a different outcome from correct pose recovery.

Allowed inputs

Predicted ligand coordinates, receptor information allowed by the protocol, and an experimental reference pose where pose recovery is scored.

Sources (2)

maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions

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)

maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions

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

Record whether a method receives an experimental bound protein, an unbound structure or a predicted receptor. PLINDER supplies related systems and versioned splits; PoseBusters supplies plausibility checks. These resources have different roles. Keep geometric validity separate from pose recovery and state any filtering of failed predictions.

Sources (2)

maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions

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)

maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions

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

Plausibility checks catch physically problematic outputs that a geometric alignment score alone may miss.
Sources (2)
maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions

Limitations and conditions

Results depend on receptor state, reference quality and failure handling. Pose accuracy does not establish binding affinity.
Sources (2)
maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions

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-pose

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) maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions
Datasets	No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicable Sources (2) maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions
Organisms	No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicable Sources (2) maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions
Assays	No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicable Sources (2) maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions
Splits	No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicable Sources (2) maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions
Allowed inputs	Predicted ligand coordinates, receptor information allowed by the protocol, and an experimental reference pose where pose recovery is scored. Sources (2) maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions
Adaptation	No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicable Sources (2) maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions
Metrics	Reference-pose error and explicitly versioned plausibility checks. A validity pass without a matching pose is a different outcome from correct pose recovery. Sources (2) maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions
Baselines	Use classical docking or learned comparators only under matched receptor and pocket information. Candidate applicability does not establish a completed run. Sources (2) maabuu/posebusters official source; plinder-org/plinder official source · PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions

Applicable tests and references

Applicability is distinct from a completed evaluation.

AutoDock Vina · proposed

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

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction 10.1021/acsomega.5c07675

Evidence locations

AF3 Fig. 1c and PoseBusters Methods; Boltz stereochemistry Table 1

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	maabuu/posebusters official source Original source ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 6236d07017493531851cce775e8ef834d4763d2f Retrieved: 2026-09-16T10:30:23.520671+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: `71fee661aba53ea2285b776d572982a57c8637275687dfe4c5b7f5113a807d0e` Hash scope: Hash scope not separately documented; inspect source record
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 ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions 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 Choose receptor state and split Predict ligand pose Check reference-pose agreement Check geometry and report failures Individual claims	maabuu/posebusters official source Original source ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 6236d07017493531851cce775e8ef834d4763d2f Retrieved: 2026-09-16T10:30:23.520671+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: `71fee661aba53ea2285b776d572982a57c8637275687dfe4c5b7f5113a807d0e` Hash scope: Hash scope not separately documented; inspect source record
Diagram steps Choose receptor state and split Predict ligand pose Check reference-pose agreement Check geometry and report failures Individual claims	plinder-org/plinder official source Original source ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions 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	maabuu/posebusters official source Original source ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 6236d07017493531851cce775e8ef834d4763d2f Retrieved: 2026-09-16T10:30:23.520671+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: `71fee661aba53ea2285b776d572982a57c8637275687dfe4c5b7f5113a807d0e` Hash scope: Hash scope not separately documented; inspect source record
Diagram title Conceptual evaluation workflow Individual claims	plinder-org/plinder official source Original source ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions 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	maabuu/posebusters official source Original source ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 6236d07017493531851cce775e8ef834d4763d2f Retrieved: 2026-09-16T10:30:23.520671+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: `71fee661aba53ea2285b776d572982a57c8637275687dfe4c5b7f5113a807d0e` Hash scope: Hash scope not separately documented; inspect source record
Entity type Task guide; concrete protocol identities remain separate. Individual claims	plinder-org/plinder official source Original source ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions 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	maabuu/posebusters official source Original source ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 6236d07017493531851cce775e8ef834d4763d2f Retrieved: 2026-09-16T10:30:23.520671+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: `71fee661aba53ea2285b776d572982a57c8637275687dfe4c5b7f5113a807d0e` 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	plinder-org/plinder official source Original source ↗ PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions 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

9 source records and release history

Chai-1 official resource · Original source · Not reported
Boltz-2 official resource · Original source · Not reported
DiffDock-L official resource · Original source · Not reported
AlphaFold 3 Server official resource · Original source · Not reported
AutoDock Vina 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
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Original source · version of record
maabuu/posebusters official source · Original source · 6236d07017493531851cce775e8ef834d4763d2f
plinder-org/plinder official source · Original source · 85b3f1cb1763530a6cfd934f4263a1777c41afa4

Download this release

Technical metadata and extraction receipts

Stable ID: catalog-task-ligand-pose

areas: molecular-interactions
entity level: task
version: Not reported
task: Protein–ligand pose
scope note: Predict the bound ligand geometry from prepared molecular inputs.
benchmark research: review date: 2026-09-17; status: primary_protocol_reviewed; primary sources: evidence-expansion-alphafold3-e627083f; evidence-expansion-boltz-stereochemistry-2025-78a77b9a; inspected locators: AF3 Fig. 1c and PoseBusters Methods; Boltz stereochemistry Table 1; searched queries: Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction 10.1021/acsomega.5c07675; 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: src-discovery-maabuu-posebusters; src-discovery-plinder-org-plinder; source locator: PoseBusters README: Usage; PLINDER README: Gold standard benchmark sets and Plinder versions; ambiguities: None recorded

Related records

applicable to: AutoDock Vina

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