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)

Length 5 Hairpins (05.0-cluster)

Cluster #structures
495 115
1677 104
396 99
1092 77
1355 70
705 64
1498 62
1491 62
1616 62
478 61
1492 60
212 60
186 60
1190 39
225 26
1188 26
1171 26
Small clusters (size < 25)
1424 (24) 1182 (24) 1138 (22) 1223 (18) 282 (16) 611 (16) 1765 (12) 1344 (12) 1364 (11) 1468 (10) 1148 (10) 50 (10) 268 (8) 826 (8) 262 (8) 1420 (7) 1041 (7) 998 (6) 271 (6) 269 (6) 854 (6) 1774 (6) 448 (5) 447 (5) 446 (5) 1467 (5) 437 (5) 432 (5) 449 (5) 1297 (5) 623 (5) 107 (5) 81 (5) 862 (5) 36 (5) 35 (5) 1435 (4) 1425 (4) 861 (4) 1347 (4) 834 (4) 815 (4) 1157 (4) 1253 (4) 279 (4) 1163 (4) 108 (4) 2 (4) 937 (3) 847 (3) 452 (3) 928 (3) 916 (3) 415 (3) 859 (3) 853 (3) 848 (3) 845 (3) 838 (3) 927 (3) 894 (3) 73 (3) 59 (3) 1079 (3) 1704 (2) 1003 (2) 1001 (2) 1701 (2) 1357 (2) 1698 (2) 972 (2) 970 (2) 965 (2) 932 (2) 924 (2) 1432 (2) 393 (2) 902 (2) 890 (2) 1397 (2) 882 (2) 1393 (2) 1391 (2) 1386 (2) 1385 (2) 1374 (2) 996 (2) 1356 (2) 955 (2) 1162 (2) 816 (2) 1323 (2) 1320 (2) 1318 (2) 87 (2) 800 (2) 1288 (2) 1286 (2) 1277 (2) 1275 (2) 1270 (2) 1269 (2) 1751 (2) 1059 (2) 1742 (2) 1740 (2) 1226 (2) 1707 (2) 198 (2) 1725 (2) 1210 (2) 930 (2) 1716 (2) 690 (2) 1710 (2) 1196 (2) 674 (2) 1692 (2) 1689 (2) 1295 (2) 1039 (2) 72 (2) 1075 (2) 49 (2) 48 (2) 1373 (2) 1055 (2) 1045 (2) 1043 (2) 1040 (2) 15 (2) 1024 (2) 938 (1) 934 (1) 678 (1) 1338 (1) 985 (1) 1272 (1) 1271 (1) 1473 (1) 948 (1) 946 (1) 943 (1) 940 (1) 939 (1) 426 (1) 425 (1) 424 (1) 423 (1) 422 (1) 421 (1) 418 (1) 929 (1) 780 (1) 926 (1) 925 (1) 923 (1) 919 (1) 1292 (1) 915 (1) 914 (1) 911 (1) 904 (1) 897 (1) 1408 (1) 1407 (1) 1406 (1) 1405 (1) 1404 (1) 1403 (1) 933 (1) 1396 (1) 659 (1) 880 (1) 877 (1) 876 (1) 875 (1) 871 (1) 870 (1) 865 (1) 864 (1) 1366 (1) 676 (1) 653 (1) 1358 (1) 842 (1) 841 (1) 830 (1) 314 (1) 892 (1) 289 (1) 1308 (1) 793 (1) 791 (1) 789 (1) 787 (1) 786 (1) 784 (1) 895 (1) 1276 (1) 1273 (1) 248 (1) 247 (1) 636 (1) 232 (1) 231 (1) 228 (1) 224 (1) 1060 (1) 884 (1) 935 (1) 199 (1) 1052 (1) 680 (1) 881 (1) 677 (1) 673 (1) 672 (1) 879 (1) 1688 (1) 1687 (1) 658 (1) 657 (1) 656 (1) 655 (1) 654 (1) 652 (1) 651 (1) 650 (1) 649 (1) 648 (1) 647 (1) 646 (1) 645 (1) 644 (1) 643 (1) 642 (1) 641 (1) 640 (1) 639 (1) 638 (1) 637 (1) 123 (1) 420 (1) 1114 (1) 1113 (1) 1112 (1) 1111 (1) 85 (1) 82 (1) 78 (1) 75 (1) 69 (1) 66 (1) 64 (1) 63 (1) 1084 (1) 1082 (1) 692 (1) 1080 (1) 1076 (1) 46 (1) 45 (1) 1579 (1) 1065 (1) 1063 (1) 1062 (1) 1061 (1) 34 (1) 1057 (1) 1056 (1) 28 (1) 1050 (1) 1048 (1) 14 (1) 13 (1) 12 (1) 11 (1) 9 (1) 8 (1) 7 (1) 5 (1) 3 (1) 0 (1)
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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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