ATOM3D
A living collection of eight curated 3D molecular-learning tasks spanning small molecules, protein interactions and mutations, ligand binding, and protein/RNA structure ranking.
Scientific task · Molecular interaction
Protein-ligand binding affinity
Predict or rank the strength of protein-small-molecule binding.
蛋白质-配体结合亲和力
Definition and search aliases
- Permanent ID
protein-ligand-binding-affinity- Aliases
- ligand affinity, binding affinity
- Deprecated aliases
- None
- Hierarchy
- Leaf task under Molecular interaction and binding
Coverage
3 benchmark families cover this task
CASP
Biennial blind community experiments that assess macromolecular structure, complex, ligand, and model-accuracy prediction against experimental structures withheld during prediction.
CASP Protein-Ligand Prediction
Formal CASP track for blind prediction of protein-ligand binding poses, binding affinity or rank, binding pockets, and pose confidence.
MoleculeNet
The original molecular-machine-learning benchmark of 17 dataset collections and more than 800 prediction endpoints spanning quantum, physicochemical, biophysical, and physiological properties.
Evidence-backed count claims
Each row keeps its original unit and basis. Rows with different units or overlapping mappings are never added.
| Benchmark | Mapped task | Coverage | Count | Version | Evidence |
|---|---|---|---|---|---|
| ATOM3D root: atom3d | Protein-ligand binding affinity official-track · high | explicitly-in-scope | 1 tasks Curated 3D benchmark datasets. | v0.2.6 as of 2026-07-22 | atom3d-paper-definition-evidence |
| CASP root: casp | Protein-ligand binding affinity official-track · high | explicitly-in-scope | Not reported CASP17 protein-ligand targets. | CASP17 as of 2026-07-21 | casp-evidence-casp17-protocol |
| CASP Protein-Ligand Prediction root: casp | Protein-ligand binding affinity official-track · high | explicitly-in-scope | Not reported CASP17 protein-ligand targets. | CASP17 as of 2026-07-21 | casp-ligand-evidence-casp17 |
| MoleculeNet root: moleculenet | Protein-ligand binding affinity official-taxonomy · high | explicitly-in-scope | 1 other Original paper dataset collections. | original-2017 | moleculenet-paper-definition-evidence |
Official evaluations connected to these benchmarks
Runs are included only for benchmark records mapped here (and formal child tracks when a mapped suite is the root). A task mapping does not imply that every run isolates this task.
| Work | Provider / class | Related runs |
|---|---|---|
| ATOM3D: Tasks On Molecules in Three Dimensions | Stanford University benchmark_creator | atom3d-creator-full |
| Assessment of Pharmaceutical Protein-Ligand Pose and Affinity Predictions in CASP16 | University of California San Diego, University of Basel, University of California Davis benchmark_creator | casp16-ligand-affinity-stage1casp16-ligand-affinity-stage2casp16-ligand-pose-regular |
| CASP16 Protein Monomer Structure Prediction Assessment | University of Texas Southwestern Medical Center, University of California Davis benchmark_creator | casp16-monomer-regular-official |
| Assessment of Protein Complex Predictions in CASP16: Are We Making Progress? | University of Texas Southwestern Medical Center, University of California Davis, Stanford University benchmark_creator | casp16-multimer-phase1-regular |
| MoleculeNet: a benchmark for molecular machine learning | Stanford University, DeepChem benchmark_creator | moleculenet-creator-full |