RNA 3D coordinate prediction

Predict RNA 3D coordinates from sequence and optional auxiliary inputs.

Task definition

Input granularity: sequence/MSA/secondary structure
Biological target: tertiary fold
Output representation: atomic coordinates
ML formulation: structure prediction
Counting notes: NR

Benchmark coverage

5 benchmarks cover this task

B11Numeric results available

RNAGym

Three core tasks plus a task-family view of the ribozyme-assay subset; the subset track is separated from the aggregate DMS-effect track.

2 benchmark-wide protocols · 7 benchmark-wide rows (not a task subtotal)

B13Numeric results available

RNA-Puzzles

Blind, rolling CASP-like assessment; puzzle count and target composition change by round.

50 benchmark-wide protocols · 5,657 benchmark-wide rows (not a task subtotal)

B14Numeric results available

CASP15 RNA

First dedicated CASP RNA season; preserve target/category filters.

9 benchmark-wide protocols · 312 benchmark-wide rows (not a task subtotal)

B15Numeric results available

CASP16 RNA/DNA

Includes RNA and nucleic-acid-containing targets; 42-target figure is reported for the richer RNA set in later assessment work.

2 benchmark-wide protocols · 258 benchmark-wide rows (not a task subtotal)

B35Numeric results available

Stanford RNA 3D Folding Challenge

Two time-separated competitions with hidden targets; submissions provide five candidate 3D structures and are evaluated best-of-five.

22 benchmark-wide protocols · 82 benchmark-wide rows (not a task subtotal)

Evaluation protocols

81 protocol units

Protocol	Track	Split / subset	Comparability
`PROT-B14-CASP15-RNA-GROUP-ASSESSMENT-CASP15--82E6EAAC-287EABFF`	CASP15 RNA group assessment B14-TR01	CASP15 RNA assessed targets ZRNA	same_table_comparable ensemble_size;candidate_count;inference_budget
`PROT-B14-CASP15-RNA-GROUP-ASSESSMENT-CASP15--A8851C66-F26E74A4`	CASP15 RNA group assessment B14-TR01	CASP15 RNA assessed targets ZTM-score	same_table_comparable ensemble_size;candidate_count;inference_budget
`PROT-B14-CASP15-RNA-GROUP-ASSESSMENT-CASP15--210E8123-DB6795A5`	CASP15 RNA group assessment B14-TR01	CASP15 RNA assessed targets ZGDT_TS	same_table_comparable ensemble_size;candidate_count;inference_budget
`PROT-B14-CASP15-RNA-GROUP-ASSESSMENT-CASP15--9025BE45-04CE2B21`	CASP15 RNA group assessment B14-TR01	CASP15 RNA assessed targets ZRMSD	same_table_comparable ensemble_size;candidate_count;inference_budget
`PROT-B14-CASP15-RNA-GROUP-ASSESSMENT-CASP15--AEB41DA3-40FA4301`	CASP15 RNA group assessment B14-TR01	CASP15 RNA assessed targets ZINF	same_table_comparable ensemble_size;candidate_count;inference_budget
`PROT-B14-CASP15-RNA-GROUP-ASSESSMENT-CASP15--1901BB2F-14A6A9B5`	CASP15 RNA group assessment B14-TR01	CASP15 RNA assessed targets ZlDDT	same_table_comparable ensemble_size;candidate_count;inference_budget
`PROT-B14-CASP15-RNA-GROUP-ASSESSMENT-CASP15--5AA03743-10A7B95B`	CASP15 RNA group assessment B14-TR01	CASP15 RNA assessed targets Zclashscore	same_table_comparable ensemble_size;candidate_count;inference_budget
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-54700889-1D1A02B0`	Stanford RNA 3D final Private leaderboard B35-TR01	RNA-Puzzles subset (n=10) Baseline	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-49EACC77-4A11C887`	Stanford RNA 3D final Private leaderboard B35-TR01	all final Private leaderboard targets (n=20) Baseline	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-54700889-19E06F39`	Stanford RNA 3D final Private leaderboard B35-TR01	RNA-Puzzles subset (n=10) Baseline	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-C9AF20C6-76611FEC`	Stanford RNA 3D final Private leaderboard B35-TR01	future PDB subset (n=10) Baseline	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-49EACC77-0712B4D4`	Stanford RNA 3D final Private leaderboard B35-TR01	all final Private leaderboard targets (n=20) Baseline	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-54700889-CF453C47`	Stanford RNA 3D final Private leaderboard B35-TR01	RNA-Puzzles subset (n=10) Baseline	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-C9AF20C6-75111AD9`	Stanford RNA 3D final Private leaderboard B35-TR01	future PDB subset (n=10) Baseline	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-49EACC77-A737D0F6`	Stanford RNA 3D final Private leaderboard B35-TR01	all final Private leaderboard targets (n=20) Baseline	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-54700889-1F0F2348`	Stanford RNA 3D final Private leaderboard B35-TR01	RNA-Puzzles subset (n=10) Baseline	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-C9AF20C6-AE2CDB9B`	Stanford RNA 3D final Private leaderboard B35-TR01	future PDB subset (n=10) Baseline	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-F723B929-760D7428`	Stanford RNA 3D final Private leaderboard B35-TR01	all final Private leaderboard targets (n=20) Kaggle	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-B8656DC9-3947F9E5`	Stanford RNA 3D final Private leaderboard B35-TR01	RNA-Puzzles subset (n=10) Kaggle	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-D92EBD2B-A17C5EAD`	Stanford RNA 3D final Private leaderboard B35-TR01	future PDB subset (n=10) Kaggle	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-F723B929-A4CE83BA`	Stanford RNA 3D final Private leaderboard B35-TR01	all final Private leaderboard targets (n=20) Kaggle	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-B8656DC9-C59716F8`	Stanford RNA 3D final Private leaderboard B35-TR01	RNA-Puzzles subset (n=10) Kaggle	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-D92EBD2B-9530DBFC`	Stanford RNA 3D final Private leaderboard B35-TR01	future PDB subset (n=10) Kaggle	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-EDFA9D07-D6B0E566`	Stanford RNA 3D final Private leaderboard B35-TR01	all final Private leaderboard targets (n=20) Post-competition	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-C82C078F-37AC0B42`	Stanford RNA 3D final Private leaderboard B35-TR01	RNA-Puzzles subset (n=10) Post-competition	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-C616D684-C5B1F0DC`	Stanford RNA 3D final Private leaderboard B35-TR01	future PDB subset (n=10) Post-competition	same_table_comparable none
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-EDFA9D07-0199F68F`	Stanford RNA 3D final Private leaderboard B35-TR01	all final Private leaderboard targets (n=20) Post-competition	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-C82C078F-868E3DDE`	Stanford RNA 3D final Private leaderboard B35-TR01	RNA-Puzzles subset (n=10) Post-competition	same_table_comparable candidate_count
`PROT-B35-STANFORD-RNA-3D-FINAL-PRIVATE-LEADE-C616D684-A46DBAA6`	Stanford RNA 3D final Private leaderboard B35-TR01	future PDB subset (n=10) Post-competition	same_table_comparable candidate_count
`PROT-SUPP-B15-CASP16-RNA-FIRST`	RNA group analysis \| first model B15-TR01	official CASP16 hidden/blind target set official RNA group-analysis target set	official_board_comparable none
`PROT-SUPP-B15-CASP16-RNA-BEST`	RNA group analysis \| best model B15-TR01	official CASP16 hidden/blind target set official RNA group-analysis target set	official_board_comparable none
`PROT-SUPP-B13-RNAPUZZLES-3312E957ACD701E5`	PZ1 official 3D assessment table B13-TR01	blind puzzle target PZ1 PZ1	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-83AB2D9D6AFA8CCD`	PZ10 official 3D assessment table B13-TR01	blind puzzle target PZ10 PZ10	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-F259CC527E645302`	PZ10tBox official 3D assessment table B13-TR01	blind puzzle target PZ10tBox PZ10tBox	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-F4625F1DE3BA1681`	PZ10tRNA official 3D assessment table B13-TR01	blind puzzle target PZ10tRNA PZ10tRNA	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-14D78B595DFF191B`	PZ11 official 3D assessment table B13-TR01	blind puzzle target PZ11 PZ11	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-F7D2CA86329F23F4`	PZ12 official 3D assessment table B13-TR01	blind puzzle target PZ12 PZ12	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-3C2A9E48EB5F7DD3`	PZ13 official 3D assessment table B13-TR01	blind puzzle target PZ13 PZ13	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-332FE3AF19C1C05D`	PZ14Bound official 3D assessment table B13-TR01	blind puzzle target PZ14Bound PZ14Bound	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-7FD3B8F947F2A4E7`	PZ14Free official 3D assessment table B13-TR01	blind puzzle target PZ14Free PZ14Free	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-235A4250D55D8A3D`	PZ15 official 3D assessment table B13-TR01	blind puzzle target PZ15 PZ15	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-8E696D261FAB244D`	PZ16a official 3D assessment table B13-TR01	blind puzzle target PZ16a PZ16a	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-7B11033390B159F3`	PZ16b official 3D assessment table B13-TR01	blind puzzle target PZ16b PZ16b	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-EE212687E166F2E1`	PZ17 official 3D assessment table B13-TR01	blind puzzle target PZ17 PZ17	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-A52527FCAFE98699`	PZ18 official 3D assessment table B13-TR01	blind puzzle target PZ18 PZ18	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-F2DBD53A171426B5`	PZ19 official 3D assessment table B13-TR01	blind puzzle target PZ19 PZ19	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-8D609133FF9A0ED0`	PZ2 official 3D assessment table B13-TR01	blind puzzle target PZ2 PZ2	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-A025C5A7B0091248`	PZ20 official 3D assessment table B13-TR01	blind puzzle target PZ20 PZ20	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-C1AF553E6543BB02`	PZ21 official 3D assessment table B13-TR01	blind puzzle target PZ21 PZ21	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-B84FA95288D6A58E`	PZ22 official 3D assessment table B13-TR01	blind puzzle target PZ22 PZ22	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-3C669F06228DD09A`	PZ22Dimer official 3D assessment table B13-TR01	blind puzzle target PZ22Dimer PZ22Dimer	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-47752C649A4EB4DD`	PZ23 official 3D assessment table B13-TR01	blind puzzle target PZ23 PZ23	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-4FED4D1851AD7699`	PZ24 official 3D assessment table B13-TR01	blind puzzle target PZ24 PZ24	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-05887D0486F7D72A`	PZ25 official 3D assessment table B13-TR01	blind puzzle target PZ25 PZ25	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-01827ECD312E4D5D`	PZ26 official 3D assessment table B13-TR01	blind puzzle target PZ26 PZ26	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-8C7E0BDE4F479807`	PZ26tBox official 3D assessment table B13-TR01	blind puzzle target PZ26tBox PZ26tBox	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-57D150BE30EFB413`	PZ26tRNA official 3D assessment table B13-TR01	blind puzzle target PZ26tRNA PZ26tRNA	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-E3F9B46B73BFF404`	PZ27 official 3D assessment table B13-TR01	blind puzzle target PZ27 PZ27	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-1EAFB9B1A0CA7E2A`	PZ27tBox official 3D assessment table B13-TR01	blind puzzle target PZ27tBox PZ27tBox	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-6F742CF9C619AB3B`	PZ27tRNA official 3D assessment table B13-TR01	blind puzzle target PZ27tRNA PZ27tRNA	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-F6FF4ABC4C0A11AE`	PZ28 official 3D assessment table B13-TR01	blind puzzle target PZ28 PZ28	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-599C3D88CA911048`	PZ28tBox official 3D assessment table B13-TR01	blind puzzle target PZ28tBox PZ28tBox	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-DE3780625C906B0A`	PZ28tRNA official 3D assessment table B13-TR01	blind puzzle target PZ28tRNA PZ28tRNA	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-9C662C44557F4E22`	PZ29 official 3D assessment table B13-TR01	blind puzzle target PZ29 PZ29	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-90502A9676F6AF50`	PZ3 official 3D assessment table B13-TR01	blind puzzle target PZ3 PZ3	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-A6811C1AC975390F`	PZ30 official 3D assessment table B13-TR01	blind puzzle target PZ30 PZ30	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-9CBCAC9FB4343021`	PZ31 official 3D assessment table B13-TR01	blind puzzle target PZ31 PZ31	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-FC40D1EADF83BAA5`	PZ32 official 3D assessment table B13-TR01	blind puzzle target PZ32 PZ32	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-3822A2433A456BE7`	PZ33 official 3D assessment table B13-TR01	blind puzzle target PZ33 PZ33	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-1BF7D7B4983707EF`	PZ34 official 3D assessment table B13-TR01	blind puzzle target PZ34 PZ34	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-ECD75F7D2DA08725`	PZ35 official 3D assessment table B13-TR01	blind puzzle target PZ35 PZ35	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-8DF1850A5187855D`	PZ36 official 3D assessment table B13-TR01	blind puzzle target PZ36 PZ36	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-DFB43C8F00172BBE`	PZ37 official 3D assessment table B13-TR01	blind puzzle target PZ37 PZ37	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-1AB577501EDBEA26`	PZ38 official 3D assessment table B13-TR01	blind puzzle target PZ38 PZ38	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-A735D039685C24F3`	PZ39 official 3D assessment table B13-TR01	blind puzzle target PZ39 PZ39	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-D0BD518D52F4775A`	PZ4 official 3D assessment table B13-TR01	blind puzzle target PZ4 PZ4	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-83674AC2AB1B3C81`	PZ5 official 3D assessment table B13-TR01	blind puzzle target PZ5 PZ5	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-6593E89FF3D79FD8`	PZ6 official 3D assessment table B13-TR01	blind puzzle target PZ6 PZ6	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-979556B28535F482`	PZ7 official 3D assessment table B13-TR01	blind puzzle target PZ7 PZ7	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-024F00B3139EBB65`	PZ8 official 3D assessment table B13-TR01	blind puzzle target PZ8 PZ8	official_board_comparable participant-specific external data;inference_budget
`PROT-SUPP-B13-RNAPUZZLES-5AC0F9290B11AB5F`	PZ9 official 3D assessment table B13-TR01	blind puzzle target PZ9 PZ9	official_board_comparable participant-specific external data;inference_budget