Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
RLooM: RNA Loop Modeling based on homology and geometric constraints - Loop Database
Current Database Version 12-19-08 (sion)
Browse Database
Hairpins (13,085) Single Strand Segments (46,361) Internal Loops (17,133) Multiloops (5,756)

Internal Loops ordered by length

Length #structures
1-1 3,728
1-2 1,248
1-3 789
1-4 353
1-5 68
10-1 60
10-29 118
10-8 118
13-15 76
15-13 76
2-1 1,248
2-2 1,930
2-3 1,091
2-4 333
2-6 311
2-7 73
29-1 118
3-1 789
3-2 1,091
3-3 4,486
3-4 706
3-5 334
3-6 596
3-7 464
3-9 62
4-1 353
4-2 333
4-3 706
4-4 960
4-5 1,133
4-6 569
4-7 130
4-9 58
5-1 68
5-3 334
5-4 1,133
5-5 598
5-6 490
5-7 280
5-8 274
6-2 311
6-3 596
6-4 569
6-5 490
6-7 153
7-2 73
7-3 464
7-4 130
7-5 280
7-6 153
7-7 196
8-1 118
8-5 274
8-8 198
9-3 62
9-4 58
9-9 292
Small sets (size < 50)
0-1 (3) 0-9 (11) 1--6 (1) 1--8 (5) 1--9 (16) 1-1 (5) 1-11 (2) 1-14 (3) 1-15 (4) 1-2 (2) 1-22 (25) 1-27 (6) 1-6 (24) 1-7 (3) 1-8 (46) 10-0 (3) 10-1 (5) 10-11 (11) 10-12 (6) 10-13 (3) 10-14 (5) 10-22 (42) 10-25 (2) 10-5 (1) 10-6 (24) 10-7 (14) 10-9 (35) 11-1 (2) 11-1 (11) 11-11 (2) 11-12 (2) 11-13 (8) 11-16 (9) 11-2 (12) 11-22 (24) 11-23 (5) 11-6 (3) 11-7 (4) 11-71 (1) 11-8 (4) 11-9 (23) 12-1 (6) 12-11 (2) 12-14 (2) 12-16 (1) 12-2 (3) 12-23 (1) 12-8 (6) 12-9 (29) 13-1 (3) 13-11 (8) 13-13 (8) 13-14 (2) 13-21 (6) 13-26 (1) 13-3 (8) 13-3 (1) 13-4 (1) 13-8 (4) 13-9 (15) 14-1 (3) 14-1 (5) 14-12 (2) 14-13 (2) 14-16 (12) 14-2 (1) 14-27 (1) 14-4 (6) 14-5 (4) 15-1 (4) 15-19 (1) 15-24 (1) 15-36 (2) 15-5 (1) 16-11 (9) 16-12 (1) 16-14 (12) 16-18 (2) 16-2 (14) 16-23 (2) 16-24 (2) 16-25 (1) 16-29 (1) 16-9 (4) 17-24 (2) 17-25 (5) 17-4 (2) 18-16 (2) 18-18 (4) 18-19 (12) 18-2 (2) 18-24 (2) 18-3 (2) 18-9 (1) 19-15 (1) 19-18 (12) 19-3 (4) 19-4 (1) 19-5 (2) 19-7 (2) 2--4 (2) 2--54 (2) 2--85 (10) 2-11 (12) 2-12 (3) 2-16 (14) 2-23 (2) 2-26 (4) 2-27 (4) 2-33 (1) 2-5 (47) 2-9 (36) 20-1 (2) 20-14 (1) 20-18 (2) 20-28 (12) 20-4 (4) 20-5 (5) 20-6 (2) 20-7 (1) 20-9 (10) 21-13 (6) 21-5 (3) 22-1 (25) 22-1 (42) 22-11 (24) 22-27 (20) 22-6 (1) 22-7 (6) 23-11 (5) 23-12 (1) 23-16 (2) 23-2 (2) 23-8 (2) 24-15 (1) 24-16 (2) 24-17 (2) 24-18 (2) 24-29 (2) 24-3 (2) 24-8 (2) 24-9 (6) 25-1 (2) 25-16 (1) 25-17 (5) 25-26 (1) 25-27 (4) 25-4 (6) 26-13 (1) 26-2 (4) 26-25 (1) 26-27 (3) 26-3 (2) 26-5 (6) 27-1 (6) 27-14 (1) 27-2 (4) 27-22 (20) 27-25 (4) 27-26 (3) 27-28 (2) 27-29 (10) 27-5 (1) 27-6 (2) 28-2 (12) 28-27 (2) 28-3 (12) 29-16 (1) 29-24 (2) 29-27 (10) 29-29 (10) 29-3 (2) 29-4 (2) 29-5 (2) 29-8 (12) 3-13 (8) 3-18 (2) 3-19 (4) 3-24 (2) 3-26 (2) 3-28 (12) 3-29 (2) 3-8 (2) 3-83 (4) 30-13 (1) 30-3 (2) 31-6 (2) 32-7 (2) 32-8 (2) 33-2 (1) 33-9 (2) 35-9 (2) 36-15 (2) 4--2 (2) 4-13 (1) 4-14 (6) 4-17 (2) 4-19 (1) 4-2 (4) 4-25 (6) 4-29 (2) 4-8 (35) 4-84 (2) 41-6 (2) 43-9 (10) 5-1 (1) 5-14 (4) 5-15 (1) 5-19 (2) 5-2 (47) 5-2 (5) 5-21 (3) 5-26 (6) 5-27 (1) 5-29 (2) 5-9 (13) 54--2 (2) 6--1 (1) 6-1 (24) 6-1 (24) 6-11 (3) 6-2 (2) 6-22 (1) 6-27 (2) 6-31 (2) 6-41 (2) 6-6 (36) 6-8 (49) 6-9 (19) 67-9 (2) 7-1 (3) 7-1 (14) 7-11 (4) 7-19 (2) 7-2 (1) 7-22 (6) 7-32 (2) 7-8 (22) 7-9 (37) 71-11 (1) 8--1 (5) 8-1 (46) 8-11 (4) 8-12 (6) 8-13 (4) 8-23 (2) 8-24 (2) 8-29 (12) 8-3 (2) 8-32 (2) 8-4 (35) 8-6 (49) 8-7 (22) 8-9 (25) 83-3 (4) 84-4 (2) 85--2 (10) 9--1 (16) 9-0 (11) 9-1 (35) 9-11 (23) 9-12 (29) 9-13 (15) 9-16 (4) 9-18 (1) 9-2 (36) 9-2 (10) 9-24 (6) 9-33 (2) 9-35 (2) 9-43 (10) 9-5 (13) 9-6 (19) 9-67 (2) 9-7 (37) 9-8 (25)
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Sequence-based queries may include NC-IUB ambiguity codes. Internal loops and multibranched loops can be searched by separating the individual loop segments with a '-' character.



Single strand search:




For a query sequence of N bases, the input range is [0,N]. The default value of 0 will be used when ambiguity codes are present in the query sequence or the input is negative. Similarly, N will be used if the input is larger than the length of the query sequence.

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Enter a 4-character pdb id. The search may be restricted to an individual chain, by attaching ':chain-id' (e.g., 2tra:A), with '%' matching any chain.

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