RNA–protein binding prediction

Predict RBP–RNA binding or binding sites.

Task definition

Input granularity: RNA sequence plus protein/assay context
Biological target: binding event/site
Output representation: probability or profile
ML formulation: classification/segmentation
Counting notes: NR

Benchmark coverage

3 benchmarks cover this task

B10Numeric results available

RNA-Scope

Board is public; DeepASmRNA and DeeReCT-PolyA/PAS are exposed as distinct tracks; verify exact release and frozen splits before comparative claims.

79 benchmark-wide protocols · 2,093 benchmark-wide rows (not a task subtotal)

B28No public numeric result

RNAglib structure–function benchmark

Seven RNA structure–function datasets; task-level splits and structural redundancy controls should be preserved.

0 benchmark-wide protocols · 0 benchmark-wide rows (not a task subtotal)

B34Numeric results available

ERNIE-RNA downstream evaluation study

One-time model study spanning 15 named data packages; PrismNet is additionally stratified into 17 HeLa RBP assays.

12 benchmark-wide protocols · 231 benchmark-wide rows (not a task subtotal)

Evaluation protocols

23 protocol units

Protocol	Track	Split / subset	Comparability
`PROT-B10-RBP-BINDING-AVERAGE-AVERAGE-OF-22-D-05D124E7-07E955EA`	RBP binding average B10-TR10	average of 22 displayed RBP entries Mean F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-AKAP1-HEPG2-F1-331E95F0`	RBP binding B10-TR10	AKAP1_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-BCLAF1-HEPG2-F1-F4D28EFF`	RBP binding B10-TR10	BCLAF1_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-DDX24-K562-F1-CB0F269F`	RBP binding B10-TR10	DDX24_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-DDX3X-HEPG2-F1-D9DFEAA8`	RBP binding B10-TR10	DDX3X_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-DDX3X-K562-F1-3602AE19`	RBP binding B10-TR10	DDX3X_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-FAM120A-K562-F1-F4B7D08A`	RBP binding B10-TR10	FAM120A_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-G3BP1-HEPG2-F1-911BDD18`	RBP binding B10-TR10	G3BP1_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-GRWD1-HEPG2-F1-3A1DAF27`	RBP binding B10-TR10	GRWD1_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-IGF2BP1-K562-F1-9EDDBD48`	RBP binding B10-TR10	IGF2BP1_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-LARP4-HEPG2-F1-8C889EDC`	RBP binding B10-TR10	LARP4_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-LIN28B-K562-F1-8DC7D3DF`	RBP binding B10-TR10	LIN28B_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-PABPC4-K562-F1-0E958620`	RBP binding B10-TR10	PABPC4_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-PPIG-HEPG2-F1-214AFA29`	RBP binding B10-TR10	PPIG_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-PUM2-K562-F1-D7BB9225`	RBP binding B10-TR10	PUM2_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-RBM15-K562-F1-234DFD93`	RBP binding B10-TR10	RBM15_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-RPS3-HEPG2-F1-D80DB76A`	RBP binding B10-TR10	RPS3_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-SND1-HEPG2-F1-24550465`	RBP binding B10-TR10	SND1_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-UPF1-HEPG2-F1-854D10A3`	RBP binding B10-TR10	UPF1_HepG2 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-UPF1-K562-F1-4D92EAFD`	RBP binding B10-TR10	UPF1_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-UCHL5-K562-F1-5CC78E7C`	RBP binding B10-TR10	UCHL5_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-YBX3-K562-F1-AF91B5D5`	RBP binding B10-TR10	YBX3_K562 F1	official_board_comparable external_data_policy;inference_budget
`PROT-B10-RBP-BINDING-YBX3-K562-F1-F87EDFB4`	RBP binding B10-TR10	YBX3_K562 F1	official_board_comparable external_data_policy;inference_budget