BioBench Atlas
Taxonomy/Protein science/Protein-ligand binding

Scientific domain

Protein-ligand binding

Binding between proteins and small molecules or other ligands.

蛋白-配体结合

9 registered benchmarks and tracks

suite1 runs

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.

PredictionClassificationRegression
competition3 runs

CAMEO

Weekly, automated, independent, blind evaluation of registered macromolecular structure-prediction servers on complete PDB entries whose experimental structures are withheld during prediction.

Prediction
competition0 runs

CASP

Biennial blind community experiments that assess macromolecular structure, complex, ligand, and model-accuracy prediction against experimental structures withheld during prediction.

Prediction
track3 runs

CASP Protein-Ligand Prediction

Formal CASP track for blind prediction of protein-ligand binding poses, binding affinity or rank, binding pockets, and pose confidence.

PredictionRegression
agentic-eval1 runs

LifeSciBench

Expert-authored, artifact-rich free-response tasks that evaluate realistic research judgment across applied life-science workflows.

Evidence synthesisRetrievalDesignGeneration
suite1 runs

MoleculeNet

The original molecular-machine-learning benchmark of 17 dataset collections and more than 800 prediction endpoints spanning quantum, physicochemical, biophysical, and physiological properties.

PredictionClassificationRegression
suite0 runs

ProteinGym

Versioned deep-mutational-scanning and clinical-variant benchmarks for protein fitness prediction and design in zero-shot and supervised regimes.

PredictionRegressionClassificationDesign
track1 runs

ProteinGym DMS Substitutions

ProteinGym track for predicting experimental fitness measurements of substitution mutants across deep-mutational-scanning assays.

PredictionRegressionClassificationDesign
dataset1 runs

ProteinLMBench

A creator-curated set of 944 protein-science multiple-choice questions with answer explanations, generated from research literature and released for evaluating text LLM protein understanding.

KnowledgeScientific reasoningPrediction

Capability coverage

Registry records tagged Protein-ligand binding, counted by capability.

CSV ↓
Accessible data table
CapabilityRecords
Knowledge1
Evidence synthesis1
Retrieval1
Prediction8
Classification4
Regression5
Design3
Generation1
Optimization3
Data analysis1
Experiment planning1
Troubleshooting1
Scientific reasoning2
Scientific communication1

Scientific Tasks in this domain

ADMET and toxicity predictionMolecular interaction and bindingProtein clinical variant interpretationProtein-complex mutation stability predictionProtein complex structure predictionProtein designProtein fitness predictionProtein-ligand binding affinityProtein-ligand binding predictionProtein-ligand functional efficacy predictionProtein-ligand pose predictionProtein model quality assessmentProtein monomer structure predictionProtein mutation-effect predictionProtein-protein interface predictionProtein residue-identity predictionProtein structure predictionRNA structure quality assessmentSmall-molecule property prediction

Task mappings are evidence-backed and may be partial for mixed suites.

Coverage-gap reading: zero counts indicate a gap in this registry, not proof that no benchmark exists. Propose a primary source through the contribution form.