Protein structure prediction

Predict or assess the three-dimensional structure of proteins or protein assemblies.

蛋白质结构预测

Definition and search aliases

Permanent ID: protein-structure
Aliases: protein structure
Deprecated aliases: None
Hierarchy: Parent task; benchmark coverage below includes its leaf tasks.

Coverage

5 benchmark families cover this task

competitionpartial

CAMEO

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

competitionpartial

CASP

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

trackcomplete

CASP Protein Multimers

Formal CASP track assessing blind protein-complex predictions, including overall folds, interfaces, stoichiometry-free phases, and model-selection phases.

suitecomplete

TAPE

A five-task benchmark for protein representation learning spanning secondary structure, residue contacts, remote homology, fluorescence, and stability.

suitecomplete

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.

trackcomplete

CASP Protein Monomers

Formal CASP track assessing blind predictions of single-protein structures and post hoc protein evaluation units against withheld experimental coordinates.

datasetpartial

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.

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
CAMEO root: cameo	Protein complex structure prediction official-taxonomy · high	explicitly-in-scope	Not reported Weekly complete-complex targets in the current CAMEO service.	current-complex-3d as of 2026-07-21	`cameo-evidence-current-help`
CASP root: casp	Protein complex structure prediction official-track · high	explicitly-in-scope	61 targets CASP17 multimer target re-releases with stoichiometry as of 2026-07-21.	CASP17 as of 2026-07-21	`casp-evidence-casp17-counts`
CASP Protein Multimers root: casp	Protein complex structure prediction official-track · high	explicitly-in-scope	61 targets CASP17 multimer target re-releases with stoichiometry as of 2026-07-21.	CASP17 as of 2026-07-21	`casp-multimer-evidence-casp17`
TAPE root: tape	Protein contact-map prediction official-taxonomy · high	explicitly-in-scope	1 tasks Supervised downstream benchmark tasks.	original-2019	`tape-paper-definition-evidence`
ATOM3D root: atom3d	Protein model quality assessment official-track · high	explicitly-in-scope	1 tasks Curated 3D benchmark datasets.	v0.2.6 as of 2026-07-22	`atom3d-paper-definition-evidence`
CAMEO root: cameo	Protein model quality assessment official-taxonomy · high	explicitly-in-scope	Not reported Weekly targets and submitted server models.	current-complex-3d as of 2026-07-21	`cameo-evidence-2024-study`
CASP root: casp	Protein model quality assessment official-track · high	explicitly-in-scope	Not reported CASP17 model-selection and accuracy-estimation targets.	CASP17 as of 2026-07-21	`casp-evidence-casp17-protocol`
CASP Protein Multimers root: casp	Protein model quality assessment official-track · high	explicitly-in-scope	Not reported CASP17 multimer model-selection evaluation units.	CASP17 as of 2026-07-21	`casp-multimer-evidence-casp17-protocol`
CASP root: casp	Protein monomer structure prediction official-track · high	explicitly-in-scope	Not reported CASP17 assessed monomer evaluation units.	CASP17 as of 2026-07-21	`casp-evidence-casp17-protocol`
CASP Protein Monomers root: casp	Protein monomer structure prediction official-track · high	explicitly-in-scope	Not reported CASP17 assessed monomer evaluation units.	CASP17 as of 2026-07-21	`casp-monomer-evidence-casp17`
TAPE root: tape	Protein secondary-structure prediction official-taxonomy · high	explicitly-in-scope	1 tasks Supervised downstream benchmark tasks.	original-2019	`tape-paper-definition-evidence`
ProteinLMBench root: proteinlmbench	Protein structure prediction official-taxonomy · high	explicitly-in-scope	Not reported Released ProteinLMBench question records.	hf-f139796	`proteinlmbench-evidence-paper`

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`
Beyond Single Chains: Benchmarking Macromolecular Complex Prediction Methods With the Continuous Automated Model EvaluatiOn (CAMEO)	SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel benchmark_creator	`cameo-2024-antibody-three-server-common` `cameo-2024-ligand-baseline-common` `cameo-2024-ppi-three-server-common`
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-stage1` `casp16-ligand-affinity-stage2` `casp16-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`
A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding	Toursun Synbio, Johns Hopkins University, University of Cambridge, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai AI Laboratory, Shanghai Jiao Tong University, UNSW Sydney benchmark_creator	`proteinlmbench-creator-full`
Evaluating Protein Transfer Learning with TAPE	University of California Berkeley benchmark_creator	`tape-creator-full`