Biology-Instructions
A multi-omics sequence-instruction suite with 21 formal predictive tasks across DNA, RNA, protein, and multi-molecule inputs; the final paper reports task-specific held-out evaluations rather than a single aggregate score.
Scientific task · Molecular interaction
Molecular interaction and binding
Predict or analyze interactions
分子相互作用与结合
Definition and search aliases
- Permanent ID
molecular-interaction-analysis- Aliases
- molecular binding
- Deprecated aliases
- None
- Hierarchy
- Parent task; benchmark coverage below includes its leaf tasks.
Coverage
8 benchmark families cover this task
Biology-Instructions Antibody-Antigen Neutralization
Binary neutralization prediction for an antibody-antigen protein-sequence pair, evaluated with Matthews correlation coefficient.
CASP17 Immune Complexes
Dedicated CASP17 category for blind prediction of antibody-antigen, nanobody-antigen, and T-cell receptor complex structures.
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.
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.
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.
ProteinGym
Versioned deep-mutational-scanning and clinical-variant benchmarks for protein fitness prediction and design in zero-shot and supervised regimes.
CAMEO
Weekly, automated, independent, blind evaluation of registered macromolecular structure-prediction servers on complete PDB entries whose experimental structures are withheld during prediction.
LAB-Bench
A practical biology-research suite of 2,457 multiple-choice questions across eight broad categories and 31 versioned task files, with public and private contamination-monitoring splits.
LAB-Bench DbQA — Viral protein–protein interactions
Retrieves predicted human interaction partners of viral proteins from P-HIPSter.
Biology-Instructions RNA-Protein Interaction Prediction
Binary interaction prediction for an RNA and protein sequence pair, evaluated with Matthews correlation coefficient.
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 |
|---|---|---|---|---|---|
| Biology-Instructions root: bioinstruction | Antibody-antigen interaction official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (Antibody-Antigen Neutralization). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions Antibody-Antigen Neutralization root: bioinstruction | Antibody-antigen interaction official-track · high | explicitly-in-scope | 26902 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-aan-evidence-paper |
| CASP17 Immune Complexes root: casp | Antibody-antigen interaction official-track · high | explicitly-in-scope | Not reported CASP17 immune-complex targets. | CASP17 as of 2026-07-21 | casp-immune-evidence-category |
| ProteinLMBench root: proteinlmbench | Molecular interaction and binding official-taxonomy · high | observed | Not reported Released ProteinLMBench question records. | hf-f139796 | proteinlmbench-evidence-paper |
| ATOM3D root: atom3d | Protein-complex mutation stability prediction official-track · high | explicitly-in-scope | 1 tasks Curated 3D benchmark datasets. | v0.2.6 as of 2026-07-22 | atom3d-paper-definition-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 |
| LifeSciBench root: lifescibench | Protein-ligand binding prediction official-taxonomy · high | explicitly-in-scope | Not reported Expert-authored benchmark tasks. | initial-release | lifescibench-evidence-taxonomy |
| ProteinGym root: proteingym | Protein-ligand binding prediction official-taxonomy · high | observed | Not reported DMS assays in the official generic Binding function category. | 1.3 | proteingym-evidence-taxonomy |
| ATOM3D root: atom3d | Protein-ligand functional efficacy prediction 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-ligand pose prediction official-taxonomy · high | explicitly-in-scope | Not reported Ligand-containing targets in the current rolling service. | current-complex-3d as of 2026-07-21 | cameo-evidence-2024-study |
| CASP root: casp | Protein-ligand pose prediction 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 pose prediction official-track · high | explicitly-in-scope | Not reported CASP17 protein-ligand targets. | CASP17 as of 2026-07-21 | casp-ligand-evidence-casp17 |
| LAB-Bench root: lab-bench | Protein-protein interaction prediction official-track · high | explicitly-in-scope | 50 questions Viral PPI formal-task questions. | repository-998a8e0 | lab-bench-evidence-paper |
| LAB-Bench DbQA — Viral protein–protein interactions root: lab-bench | Protein-protein interaction prediction official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-dbqa-viral-ppi-evidence-paper |
| LifeSciBench root: lifescibench | Protein-protein interaction prediction official-taxonomy · high | explicitly-in-scope | Not reported Expert-authored benchmark tasks. | initial-release | lifescibench-evidence-taxonomy |
| ATOM3D root: atom3d | Protein-protein interface prediction official-track · high | explicitly-in-scope | 1 tasks Curated 3D benchmark datasets. | v0.2.6 as of 2026-07-22 | atom3d-paper-definition-evidence |
| Biology-Instructions root: bioinstruction | RNA-protein interaction prediction official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (RNA-Protein Interaction Prediction). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions RNA-Protein Interaction Prediction root: bioinstruction | RNA-protein interaction prediction official-track · high | explicitly-in-scope | 20824 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-rpi-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.