Configuration

Vina

AutoDock Vina is a conventional docking/scoring comparator in the DiffDock-NMDN study.

Sources

Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Data Sets/Evaluation Metrics/CASF-2016 (paragraph 3); DiffDock-NMDN Blind Docking and Virtual Screening Protocol (paragraph 1)

1 evaluation · 1 result

How it worksEvaluated procedure (conceptual)

Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.

Sources

Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1)

Overview

Model type

Empirical docking algorithm; this record is the paper-specific evaluated configuration.

Sources

ccsb-scripps/AutoDock-Vina README.md · README.md model description

Biological inputs

Receptor and ligand structural information under the study’s search-box protocol

Sources

Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Methods/Interaction Module/Calculation of Protein–Ligand Pair Contributions (paragraph 8); Methods/Interaction Module/Calculation of Protein–Ligand Pair Contributions (paragraph 6)

Outputs

Docked poses and empirical docking scores

Sources

Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Results and Discussion/DiffDock-NMDN Blind Docking Protocol (paragraph 4); Data Sets/Evaluation Metrics/CASF-2016 (paragraph 2)

Access

Official upstream implementation and usage documentation: https://github.com/ccsb-scripps/AutoDock-Vina/blob/3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645/README.md. This pinned documentation revision is not automatically the evaluated weight revision.

Sources

ccsb-scripps/AutoDock-Vina README.md · README.md; installation, model download and usage instructions

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

Filter evaluations

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: Vina	Task: Protein–ligand virtual screening Dataset: CASF-2016 blind docked poses	42.1 Forward-screening success rate % · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Vina: Protein–ligand virtual screening Vina scoring on the same DiffDock-NMDN blind docked poses; not ligand-pose RMSD. Aggregation: Not reported Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Table 2, Vina scoring row, success rate (%) column

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

Use this model

How it works, versions and access

How it works

How the evaluated method works

A docking search and empirical scoring function estimate ligand poses and scores from receptor/ligand structures.

Sources

Underlying method and version boundaries

AutoDock Vina performs molecular docking using an empirical scoring function and an optimisation procedure. The scoring-function choice, search space and supplied receptor structure define the evaluation setting.

Sources

ccsb-scripps/AutoDock-Vina README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revision

What was evaluated

The linked evaluation record identifies Vina: Protein–ligand virtual screening. Its dataset, split, adaptation and evidence origin remain attached to the reported results.

Sources

Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-044

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

Provides a non-foundation-model docking reference.
Sources
Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Methods/Normalized Mixture Density Network Module/Inference (paragraph 2); Ablation Study/Normalization Terms and Selection of Reference Distance (paragraph 1)

Limitations and conditions

Docking scores are approximations and must not be interpreted as experimentally measured affinities.
Sources
Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Methods/Interaction Module/Enhancing the Virtual Screening Capability of pKd Score (paragraph 2); Data Sets/Evaluation Metrics/CASF-2016 (paragraph 2)

Profile review details

Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.

Stable record: reported-model-1e51ccbfd2de61

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · 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	Empirical docking algorithm; this record is the paper-specific evaluated configuration. Sources ccsb-scripps/AutoDock-Vina README.md · README.md model description
Architecture / procedure	A docking search and empirical scoring function estimate ligand poses and scores from receptor/ligand structures. Sources Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1)
Biological inputs	Receptor and ligand structural information under the study’s search-box protocol Sources Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Methods/Interaction Module/Calculation of Protein–Ligand Pair Contributions (paragraph 8); Methods/Interaction Module/Calculation of Protein–Ligand Pair Contributions (paragraph 6)
Outputs	Docked poses and empirical docking scores Sources Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Results and Discussion/DiffDock-NMDN Blind Docking Protocol (paragraph 4); Data Sets/Evaluation Metrics/CASF-2016 (paragraph 2)
Parameters	Not applicable to a neural parameter count: this is an empirical scoring and conformational search procedure. · Not applicable Sources Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Introduction (paragraph 2); Introduction (paragraph 1)
Known versions / configuration	Vina is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sources Sources Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label.
Training data / fitting	No task-specific neural fitting is described for this docking comparator; the scoring function and receptor/ligand preparation define the procedure. Sources Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 5)
Context limits	Not applicable to a sequence-token limit: receptor coordinates, ligand conformers and the defined search region determine the input. · Not applicable Sources Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Methods/Normalized Mixture Density Network Module/Inference (paragraph 1); Methods/Normalized Mixture Density Network Module/Inference (paragraph 4)
Access	Official upstream implementation and usage documentation: https://github.com/ccsb-scripps/AutoDock-Vina/blob/3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645/README.md. This pinned documentation revision is not automatically the evaluated weight revision. Sources ccsb-scripps/AutoDock-Vina README.md · README.md; installation, model download and usage instructions
Code licence	Apache 2.0 (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence). Sources ccsb-scripps/AutoDock-Vina LICENSE · LICENSE; complete licence text
Weights licence	Not applicable: no pretrained neural checkpoint is used. · Not applicable Sources Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Methods/Normalized Mixture Density Network Module/Protein–ligand NMDN Module Architecture (paragraph 3); Methods/Normalized Mixture Density Network Module/Inference (paragraph 6)

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.

20 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 input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims	Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening Original source ↗ Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:41:16.552697+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `194b21478aaedd9a7384cabb8b0040ca5b6a4938f4d275627b86a6b787affc20` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps Receptor and ligand structural information under the study’s search-box protocol Vina Docked poses and empirical docking scores Individual claims	Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening Original source ↗ Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:41:16.552697+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `194b21478aaedd9a7384cabb8b0040ca5b6a4938f4d275627b86a6b787affc20` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Evaluated procedure (conceptual) Individual claims	Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening Original source ↗ Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:41:16.552697+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `194b21478aaedd9a7384cabb8b0040ca5b6a4938f4d275627b86a6b787affc20` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Model type Empirical docking algorithm; this record is the paper-specific evaluated configuration. Individual claims	ccsb-scripps/AutoDock-Vina README.md Original source ↗ README.md model description Version: 3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645 Retrieved: 2026-09-16T20:00:01.500953+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `4f1728521ab79de1c33e1cf8605b31037effed5de2a2fbbccba58d7b0a005ae7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Architecture / procedure A docking search and empirical scoring function estimate ligand poses and scores from receptor/ligand structures. Individual claims	Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening Original source ↗ Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:41:16.552697+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `194b21478aaedd9a7384cabb8b0040ca5b6a4938f4d275627b86a6b787affc20` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Weights licence Not applicable: no pretrained neural checkpoint is used. Individual claims	Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening Original source ↗ Methods/Normalized Mixture Density Network Module/Protein–ligand NMDN Module Architecture (paragraph 3); Methods/Normalized Mixture Density Network Module/Inference (paragraph 6) Version: version of record Retrieved: 2026-09-16T10:41:16.552697+00:00	inapplicable automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `194b21478aaedd9a7384cabb8b0040ca5b6a4938f4d275627b86a6b787affc20` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Biological inputs Receptor and ligand structural information under the study’s search-box protocol Individual claims	Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening Original source ↗ Methods/Interaction Module/Calculation of Protein–Ligand Pair Contributions (paragraph 8); Methods/Interaction Module/Calculation of Protein–Ligand Pair Contributions (paragraph 6) Version: version of record Retrieved: 2026-09-16T10:41:16.552697+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `194b21478aaedd9a7384cabb8b0040ca5b6a4938f4d275627b86a6b787affc20` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Outputs Docked poses and empirical docking scores Individual claims	Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening Original source ↗ Results and Discussion/DiffDock-NMDN Blind Docking Protocol (paragraph 4); Data Sets/Evaluation Metrics/CASF-2016 (paragraph 2) Version: version of record Retrieved: 2026-09-16T10:41:16.552697+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `194b21478aaedd9a7384cabb8b0040ca5b6a4938f4d275627b86a6b787affc20` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters Not applicable to a neural parameter count: this is an empirical scoring and conformational search procedure. Individual claims	Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening Original source ↗ Introduction (paragraph 2); Introduction (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:41:16.552697+00:00	inapplicable automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `194b21478aaedd9a7384cabb8b0040ca5b6a4938f4d275627b86a6b787affc20` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Known versions / configuration Vina is the comparison-table label; that label does not specify an immutable weight revision. Individual claims	Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening Original source ↗ Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: version of record Retrieved: 2026-09-16T10:41:16.552697+00:00	unreported automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `194b21478aaedd9a7384cabb8b0040ca5b6a4938f4d275627b86a6b787affc20` 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: needs review

3 source records and release history

Normalized Protein–Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening · Original source · version of record
ccsb-scripps/AutoDock-Vina README.md · Original source · 3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645
ccsb-scripps/AutoDock-Vina LICENSE · Original source · 3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645

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Technical metadata and extraction receipts

Stable ID: reported-model-1e51ccbfd2de61

areas: molecular-interactions
entity level: method
version: Not reported
reported name: Vina
historical missing metadata: version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
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 source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: nmdn-2025; evidence-reported-base-vina-readme-md; source locator: Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1) | README.md model description | Data Sets/Evaluation Metrics/CASF-2016 (paragraph 3); DiffDock-NMDN Blind Docking and Virtual Screening Protocol (paragraph 1); ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

Related records

model: Vina: Protein–ligand virtual screening

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