Model type
Empirical docking algorithm; this record is the paper-specific evaluated configuration.
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)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)At a glance
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)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Vina: Protein–ligand virtual screening Vina scoring on the same DiffDock-NMDN blind docked poses; not ligand-pose RMSD. Independent external evaluation · Evaluation metadata: needs review | ||
| 42.1 Forward-screening success rate Unit: % · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedNormalized 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. |
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
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)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 revisionWhat 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-044Strengths 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-1e51ccbfd2de61Specifications
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.
| Property | Description and evidence |
|---|---|
| Model type | Empirical docking algorithm; this record is the paper-specific evaluated configuration.Sourcesccsb-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.SourcesNormalized 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 protocolSourcesNormalized 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 scoresSourcesNormalized 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 applicableSourcesNormalized 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 sourcesSourcesNormalized 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.SourcesNormalized 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 applicableSourcesNormalized 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.Sourcesccsb-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).Sourcesccsb-scripps/AutoDock-Vina LICENSE · LICENSE; complete licence text |
| Weights licence | Not applicable: no pretrained neural checkpoint is used. · Not applicableSourcesNormalized 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 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
| 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 Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | 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) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Empirical docking algorithm; this record is the paper-specific evaluated configuration. Individual claims | ccsb-scripps/AutoDock-Vina README.md README.md model description Version: 3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645 | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 Methods/Normalized Mixture Density Network Module/Training Loss for the NMDN Modules (paragraph 3); Conclusions (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 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 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 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 | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Docked poses and empirical docking scores Individual claims | 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) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 Introduction (paragraph 2); Introduction (paragraph 1) Version: version of record | inapplicable automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: version of record | unreported automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · 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
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.