# This table contains background probabilities for several different # local structure alphabets, using the dunbrack-in-scop set of 1298 chains # as the training set. # Alphabets that may be worth including: # DSSP.alphabet: Name = DSSP # DSSP.alphabet: Name = EBGHSTL (usual reduction of DSSP, eliminating I) # DSSP.alphabet: Name = STRIDE # DSSP.alphabet: Name = EBGHTL (usual reduction of STRIDE, eliminating I) # abs_sa.alphabet: Name = abs_sa8 # abs_sa.alphabet: Name = abs_sa7 # alpha.alphabet: Name = alpha11 # burial-sa.alphabet: Name = abs_sa_CB_burial_12_7 # burial.alphabet: Name = CB_burial_6.5_7 # burial.alphabet: Name = CB_burial_8_7 # burial.alphabet: Name = CB_burial_10_7 # burial.alphabet: Name = CB_burial_12_7 # burial.alphabet: Name = CB_burial_14_7 # burial.alphabet: Name = CB_burial_16_7 # burial.alphabet: Name = CA_burial_6.5_7 # burial.alphabet: Name = CA_burial_8_7 # burial.alphabet: Name = CA_burial_10_7 # burial.alphabet: Name = CA_burial_12_7 # burial.alphabet: Name = CA_burial_14_7 # burial.alphabet: Name = dry_burial_6.5_7 # burial.alphabet: Name = dry_burial_8_7 # burial.alphabet: Name = dry_burial_10_7 # burial.alphabet: Name = dry_burial_12_7 # burial.alphabet: Name = dry_burial_14_7 # burial.alphabet: Name = wet_burial_6.5_7 # burial.alphabet: Name = wet_burial_8_7 # burial.alphabet: Name = wet_burial_10_7 # burial.alphabet: Name = wet_burial_12_7 # burial.alphabet: Name = burial_6.5_5 # burial.alphabet: Name = burial_6.5_11 # burial.alphabet: Name = burial_6.5_9 # burial.alphabet: Name = burial_6.5_7 # burial.alphabet: Name = burial_8_7 # burial.alphabet: Name = burial_9_7 # burial.alphabet: Name = burial_10_7 # burial.alphabet: Name = burial_12_7 # bystroff.alphabet: Name = Bystroff # chi.alphabet: Name = chi1_3 # chi.alphabet: Name = chi1_7 # chi.alphabet: Name = chi1_5 # gamma.alphabet: Name = gamma_2 # pb.alphabet: Name = pb # rel_sa.alphabet: Name = rel_sa7 # rel_sa.alphabet: Name = rel_sa2 # rel_sa.alphabet: Name = rel_sa3 # rel_sa.alphabet: Name = rel_sa10 # str.alphabet: Name = str # str.alphabet: Name = str2 # tco.alphabet: Name = tco # two-spot-burial.alphabet: Name = near-backbone-7 # two-spot-burial.alphabet: Name = near-backbone-10 # two-spot-burial.alphabet: Name = near-backbone-11 # two-spot-burial.alphabet: Name = way-back-7 # two-spot-burial.alphabet: Name = way-back-11 # The following are omitted because the names are bad-- # they have too many possible meanings: # (reductions of both DSSP and STRIDE) # DSSP.alphabet: Name = EHL # DSSP.alphabet: Name = EHL2 (use dssp_ehl2 or stride_ehl2) # DSSP.alphabet: Name = EHTL # DSSP.alphabet: Name = EHTL2 # DSSP.alphabet: Name = EBHTL # (unknown meaning) # angle.alphabet: Name = Angle # angle.alphabet: Name = redAngle # akp.alphabet: Name = akp # pmt.alphabet: Name = PMTN (old name for chi1_3???) ClassName = BackgroundProbs Alphabet = way-back-11 Order = A B C D E F G H I J K Probs = 0.0953 0.0672 0.0657 0.1211 0.1120 0.0897 0.0946 0.1084 0.0800 0.1031 0.0630 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = near-backbone-11 Order = A B C D E F G H I J K Probs = 0.0933 0.0738 0.0766 0.1089 0.0918 0.0869 0.1229 0.0937 0.0988 0.0855 0.0679 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = rel_sa10 Order = A B C D E F G H I J Probs = 0.1770 0.0951 0.0850 0.0908 0.0978 0.1094 0.1172 0.1103 0.0774 0.0401 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = CB_burial_12_7 Order = A B C D E F G Probs = 0.1311 0.1524 0.1693 0.1607 0.1668 0.1459 0.0738 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = CB_burial_14_7 Order = A B C D E F G Probs = 0.1600 0.1608 0.1458 0.1593 0.1481 0.1420 0.0839 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = ExtAA Order = A C D E F G H I K L M N P Q R S T V W Y Probs = 0.0824 0.0148 0.0588 0.0647 0.0395 0.0741 0.0224 0.0566 0.0596 0.0892 0.0220 0.0447 0.0460 0.0393 0.0498 0.0600 0.0564 0.0704 0.0141 0.0352 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = abs_sa7 Order = B C D E F G H Probs = 0.1408 0.1370 0.1612 0.1252 0.1452 0.1419 0.1487 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = alpha11 Order = A B C D E F G H I S T Probs = 0.0837 0.1143 0.0535 0.0251 0.1516 0.0186 0.0346 0.3321 0.0794 0.0724 0.0346 EndClassName = BackgroundProbs // I can't identify this alphabet! // ClassName = BackgroundProbs // Alphabet = ang // Order = B D E G H K L T Y Z // Probs = 0.1739 0.0216 0.1747 0.0847 0.4227 0.0237 0.0233 0.0259 0.0368 0.0129 // EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = Bystroff Order = C D E G H L N P S T Y Probs = 0.0023 0.0218 0.1761 0.0818 0.4240 0.0226 0.0263 0.1716 0.0128 0.0233 0.0375 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = chi1_3 Order = M P T Probs = 0.5215 0.1711 0.3074 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = dry_burial_6.5_7 Order = A B C D E F G Probs = 0.1405 0.1454 0.1519 0.1527 0.1663 0.1620 0.0813 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = dry_burial_8_7 Order = A B C D E F G Probs = 0.1733 0.1610 0.1417 0.1338 0.1448 0.1391 0.1064 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = dry_burial_12_7 Order = A B C D E F G Probs = 0.1861 0.1542 0.1476 0.1411 0.1397 0.1343 0.0969 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = DSSP Order = B E G H I L S T Probs = 0.0121 0.2154 0.0387 0.3280 0.0002 0.2025 0.0882 0.1149 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = EBGHSTL Order = B E G H L S T Probs = 0.0121 0.2154 0.0387 0.3282 0.2025 0.0882 0.1149 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = str Order = A B C E G H I M P Q S T Z Probs = 0.0466 0.0120 0.2024 0.0106 0.0388 0.3279 0.0002 0.0112 0.0188 0.0291 0.0881 0.1149 0.0993 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = str2 Order = A B C E G H M P Q S T Y Z Probs = 0.0466 0.0120 0.2024 0.0106 0.0388 0.3280 0.0112 0.0188 0.0291 0.0881 0.1149 0.0399 0.0594 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = dssp_ehl2 Order = E H L Probs = 0.2277 0.3668 0.4055 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = STRIDE Order = B C E G H I T Probs = 0.0114 0.1810 0.2221 0.0384 0.3420 0.0001 0.2049 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = EBGHTL Order = B C E G H T Probs = 0.0114 0.1810 0.2221 0.0384 0.3421 0.2049 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = stride_ehl2 Order = E H L Probs = 0.2336 0.3805 0.3859 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = tco Order = E F G H Probs = 0.2902 0.1566 0.1111 0.4421 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = wet_burial_6.5_7 Order = A B C D E F G Probs = 0.3159 0.1513 0.1236 0.1156 0.1059 0.1000 0.0876 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = pb # This is de Brevern's protein blocks. Order = A B C D E F G H I J K L M N O P Probs = 0.0383 0.0449 0.0846 0.1883 0.0219 0.0668 0.0121 0.0219 0.0155 0.0088 0.0543 0.0531 0.3121 0.0185 0.0252 0.0336 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = gamma_2 Order = L M Probs = 0.5352 0.4648 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = n_sep Order = A B C D G H I J K L M N P Q R S T U V W Probs = 0.1594 0.0142 0.0840 0.3824 0.0692 0.2441 0.0124 0.0013 0.0041 0.0038 0.0027 0.0014 0.0045 0.0036 0.0022 0.0007 0.0032 0.0033 0.0023 0.0014 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = o_sep Order = A B C D G H I J K L M N P Q R S T U V W Probs = 0.1430 0.0776 0.0742 0.3968 0.0588 0.2136 0.0063 0.0008 0.0037 0.0033 0.0022 0.0011 0.0037 0.0029 0.0020 0.0006 0.0030 0.0030 0.0021 0.0013 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = n_notor Order = A B G H M N P S Probs = 0.0529 0.0808 0.0692 0.2441 0.0142 0.3824 0.0725 0.0840 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = o_notor Order = A B G H M N P S Probs = 0.0482 0.0693 0.0588 0.2136 0.0776 0.3968 0.0614 0.0742 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = n_notor2 Order = A B F G H I J M N P S Probs = 0.0509 0.0803 0.0078 0.0692 0.2441 0.0124 1.e-07 0.0064 0.3824 0.0625 0.0840 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = o_notor2 Order = A B F G H I J M N P S Probs = 0.0471 0.0689 0.0062 0.0588 0.2136 0.0063 0.0031 0.0683 0.3968 0.0565 0.0742 EndClassName = BackgroundProbs ClassName = BackgroundProbs Alphabet = CB8-sep9 Order = A B C D E F G H I J K L M N Probs = 0.1649 0.1000 0.0945 0.1076 0.1159 0.1019 0.0846 0.0692 0.0545 0.0407 0.0304 0.0198 0.0102 0.0058 EndClassName = BackgroundProbs # ClassName = BackgroundProbs # Alphabet = # Order = # Probs = # EndClassName = BackgroundProbs