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Add example Jupyter notebook for analyzing P2Rank output

Browse Source 
Add notebook loading _predictions.csv and _residues.csv with example
data from predict_1fbl. Clean up CSV formatting: remove padding from
values, add fmtCsv() without leading spaces for CSV output.
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rdk
2026-03-09 12:05:00 +01:00
parent 61b8863c27
commit fdebd71daf
14 changed files with 12221 additions and 22 deletions
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name, rank, score, probability, sas_points, surf_atoms, center_x, center_y, center_z, residue_ids, surf_atom_ids
pocket1, 1, 9.77, 0.525, 70, 40, 70.5274, 83.4375, -11.5099, A_103 A_180 A_181 A_182 A_183 A_184 A_186 A_214 A_215 A_218 A_219 A_222 A_226 A_227 A_228 A_238 A_239 A_240, 32 33 651 658 659 664 670 676 679 692 700 929 934 938 942 943 958 959 960 961 962 963 971 972 989 991 992 993 994 1016 1026 1033 1035 1036 1106 1112 1118 1119 1122 1124
pocket2, 2, 3.04, 0.101, 37, 18, 89.2267, 98.6419, 26.7534, A_337 A_339 A_341 A_348 A_357 A_360 A_362 A_366 A_367 A_368 A_400 A_402, 1890 1891 1909 1910 1926 1991 2064 2091 2092 2109 2144 2150 2151 2161 2163 2426 2439 2444
pocket3, 3, 2.94, 0.095, 34, 15, 61.1038, 70.7493, -13.6472, A_119 A_156 A_160 A_162 A_164 A_168 A_191 A_194 A_196, 171 172 173 472 499 501 514 515 532 560 728 730 746 760 761
pocket4, 4, 1.87, 0.037, 27, 17, 90.8572, 95.9207, 10.7905, A_290 A_291 A_293 A_304 A_320 A_321 A_340 A_353 A_354, 1488 1489 1490 1497 1499 1513 1619 1620 1756 1757 1766 1769 1917 2030 2031 2034 2035
1 name rank score probability sas_points surf_atoms center_x center_y center_z residue_ids surf_atom_ids
2 pocket1 1 9.77 0.525 70 40 70.5274 83.4375 -11.5099 A_103 A_180 A_181 A_182 A_183 A_184 A_186 A_214 A_215 A_218 A_219 A_222 A_226 A_227 A_228 A_238 A_239 A_240 32 33 651 658 659 664 670 676 679 692 700 929 934 938 942 943 958 959 960 961 962 963 971 972 989 991 992 993 994 1016 1026 1033 1035 1036 1106 1112 1118 1119 1122 1124
3 pocket2 2 3.04 0.101 37 18 89.2267 98.6419 26.7534 A_337 A_339 A_341 A_348 A_357 A_360 A_362 A_366 A_367 A_368 A_400 A_402 1890 1891 1909 1910 1926 1991 2064 2091 2092 2109 2144 2150 2151 2161 2163 2426 2439 2444
4 pocket3 3 2.94 0.095 34 15 61.1038 70.7493 -13.6472 A_119 A_156 A_160 A_162 A_164 A_168 A_191 A_194 A_196 171 172 173 472 499 501 514 515 532 560 728 730 746 760 761
5 pocket4 4 1.87 0.037 27 17 90.8572 95.9207 10.7905 A_290 A_291 A_293 A_304 A_320 A_321 A_340 A_353 A_354 1488 1489 1490 1497 1499 1513 1619 1620 1756 1757 1766 1769 1917 2030 2031 2034 2035

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chain, residue_label, residue_name, score, zscore, probability, pocket
A, 100, PHE, 0.5863, -0.0527, 0.0491, 0
A, 101, VAL, 0.1968, -0.2697, 0.0067, 0
A, 102, LEU, 0.0989, -0.3243, 0.0023, 0
A, 103, THR, 0.6058, -0.0418, 0.0523, 1
A, 104, PRO, 0.0206, -0.3680, 0.0005, 0
A, 105, GLY, 0.0092, -0.3743, 0.0003, 0
A, 106, ASN, 0.0249, -0.3656, 0.0006, 0
A, 107, PRO, 0.0174, -0.3698, 0.0005, 0
A, 108, ARG, 0.0233, -0.3664, 0.0005, 0
A, 109, TRP, 0.0864, -0.3313, 0.0019, 0
A, 110, GLU, 0.0384, -0.3581, 0.0008, 0
A, 111, ASN, 0.0742, -0.3381, 0.0016, 0
A, 112, THR, 0.0271, -0.3643, 0.0006, 0
A, 113, HIS, 0.0742, -0.3381, 0.0016, 0
A, 114, LEU, 0.0632, -0.3442, 0.0013, 0
A, 115, THR, 0.0382, -0.3582, 0.0008, 0
A, 116, TYR, 0.0684, -0.3413, 0.0014, 0
A, 117, ARG, 0.0210, -0.3678, 0.0005, 0
A, 118, ILE, 0.0366, -0.3590, 0.0008, 0
A, 119, GLU, 1.0303, 0.1948, 0.1491, 3
A, 120, ASN, 0.0779, -0.3360, 0.0017, 0
A, 121, TYR, 0.1071, -0.3197, 0.0026, 0
A, 122, THR, 0.0163, -0.3704, 0.0004, 0
A, 123, PRO, 0.0185, -0.3691, 0.0005, 0
A, 124, ASP, 0.0206, -0.3680, 0.0005, 0
A, 125, LEU, 0.1977, -0.2693, 0.0067, 0
A, 126, SER, 0.0248, -0.3656, 0.0006, 0
A, 127, ARG, 0.0981, -0.3248, 0.0023, 0
A, 128, GLU, 0.0397, -0.3573, 0.0008, 0
A, 129, ASP, 0.2691, -0.2295, 0.0115, 0
A, 130, VAL, 0.0862, -0.3314, 0.0019, 0
A, 131, ASP, 0.0672, -0.3420, 0.0014, 0
A, 132, ARG, 0.2657, -0.2313, 0.0112, 0
A, 133, ALA, 0.3319, -0.1945, 0.0168, 0
A, 134, ILE, 0.0525, -0.3502, 0.0011, 0
A, 135, GLU, 0.1450, -0.2986, 0.0041, 0
A, 136, LYS, 0.6173, -0.0354, 0.0542, 0
A, 137, ALA, 0.0002, -0.3794, 0.0002, 0
A, 138, PHE, 0.0770, -0.3366, 0.0017, 0
A, 139, GLN, 0.1328, -0.3054, 0.0036, 0
A, 140, LEU, 0.1585, -0.2911, 0.0047, 0
A, 141, TRP, 0.0676, -0.3418, 0.0014, 0
A, 142, SER, 0.1231, -0.3108, 0.0032, 0
A, 143, ASN, 0.1959, -0.2703, 0.0066, 0
A, 144, VAL, 0.1321, -0.3058, 0.0035, 0
A, 145, SER, 0.0061, -0.3760, 0.0003, 0
A, 146, PRO, 0.0286, -0.3635, 0.0006, 0
A, 147, LEU, 0.1067, -0.3200, 0.0026, 0
A, 148, THR, 0.1447, -0.2988, 0.0041, 0
A, 149, PHE, 0.1362, -0.3036, 0.0037, 0
A, 150, THR, 0.1135, -0.3162, 0.0028, 0
A, 151, LYS, 0.1105, -0.3179, 0.0027, 0
A, 152, VAL, 0.0485, -0.3524, 0.0010, 0
A, 153, SER, 0.0704, -0.3402, 0.0015, 0
A, 154, GLU, 0.0210, -0.3677, 0.0005, 0
A, 155, GLY, 0.0064, -0.3759, 0.0003, 0
A, 156, GLN, 0.0271, -0.3644, 0.0006, 3
A, 157, ALA, 0.0219, -0.3672, 0.0005, 0
A, 158, ASP, 0.0828, -0.3333, 0.0018, 0
A, 159, ILE, 0.0033, -0.3776, 0.0003, 0
A, 160, MET, 0.9464, 0.1481, 0.1269, 3
A, 161, ILE, 0.7581, 0.0431, 0.0818, 0
A, 162, SER, 1.0132, 0.1853, 0.1445, 3
A, 163, PHE, 0.0534, -0.3497, 0.0011, 0
A, 164, VAL, 0.1232, -0.3108, 0.0032, 3
A, 165, ARG, 0.0402, -0.3570, 0.0008, 0
A, 166, GLY, 0.0114, -0.3731, 0.0004, 0
A, 167, ASP, 0.0143, -0.3715, 0.0004, 0
A, 168, HIS, 0.1673, -0.2862, 0.0051, 3
A, 169, ARG, 0.0373, -0.3586, 0.0008, 0
A, 170, ASP, 0.3326, -0.1941, 0.0169, 0
A, 171, ASN, 0.0857, -0.3317, 0.0019, 0
A, 172, SER, 0.2911, -0.2172, 0.0133, 0
A, 173, PRO, 0.0421, -0.3560, 0.0009, 0
A, 174, PHE, 0.0574, -0.3475, 0.0012, 0
A, 175, ASP, 0.0343, -0.3604, 0.0007, 0
A, 176, GLY, 0.0088, -0.3745, 0.0003, 0
A, 177, PRO, 0.0826, -0.3334, 0.0018, 0
A, 178, GLY, 0.2319, -0.2502, 0.0089, 0
A, 179, GLY, 0.2707, -0.2285, 0.0116, 0
A, 180, ASN, 1.6667, 0.5495, 0.3284, 1
A, 181, LEU, 0.5081, -0.0963, 0.0370, 1
A, 182, ALA, 3.4334, 1.5343, 0.6739, 1
A, 183, HIS, 3.4902, 1.5660, 0.6815, 1
A, 184, ALA, 2.6624, 1.1046, 0.5529, 1
A, 185, PHE, 0.9324, 0.1403, 0.1234, 0
A, 186, GLN, 0.3475, -0.1858, 0.0182, 1
A, 187, PRO, 0.0494, -0.3519, 0.0010, 0
A, 188, GLY, 0.0776, -0.3362, 0.0017, 0
A, 189, PRO, 0.0802, -0.3348, 0.0017, 0
A, 190, GLY, 0.0561, -0.3482, 0.0011, 0
A, 191, ILE, 0.9980, 0.1768, 0.1404, 3
A, 192, GLY, 0.0692, -0.3409, 0.0015, 0
A, 193, GLY, 0.0119, -0.3728, 0.0004, 0
A, 194, ASP, 0.9252, 0.1363, 0.1216, 3
A, 195, ALA, 0.6133, -0.0376, 0.0535, 0
A, 196, HIS, 0.9880, 0.1713, 0.1377, 3
A, 197, PHE, 0.0000, -0.3795, 0.0002, 0
A, 198, ASP, 0.0007, -0.3790, 0.0002, 0
A, 199, GLU, 0.0204, -0.3681, 0.0005, 0
A, 200, ASP, 0.0313, -0.3620, 0.0007, 0
A, 201, GLU, 0.0563, -0.3481, 0.0012, 0
A, 202, ARG, 0.1073, -0.3196, 0.0026, 0
A, 203, TRP, 0.0215, -0.3675, 0.0005, 0
A, 204, THR, 0.3933, -0.1603, 0.0228, 0
A, 205, LYS, 0.6021, -0.0438, 0.0516, 0
A, 206, ASN, 0.4865, -0.1083, 0.0341, 0
A, 207, PHE, 0.1933, -0.2717, 0.0065, 0
A, 208, ARG, 0.1135, -0.3162, 0.0028, 0
A, 209, ASP, 0.2679, -0.2302, 0.0114, 0
A, 210, TYR, 0.3235, -0.1992, 0.0160, 0
A, 211, ASN, 0.5608, -0.0668, 0.0450, 0
A, 212, LEU, 0.2492, -0.2405, 0.0101, 0
A, 213, TYR, 0.6073, -0.0410, 0.0525, 0
A, 214, ARG, 1.0201, 0.1892, 0.1464, 1
A, 215, VAL, 1.1105, 0.2395, 0.1711, 1
A, 216, ALA, 0.0158, -0.3706, 0.0004, 0
A, 217, ALA, 0.0000, -0.3795, 0.0002, 0
A, 218, HIS, 3.7453, 1.7082, 0.7135, 1
A, 219, GLU, 3.7748, 1.7246, 0.7170, 1
A, 220, LEU, 0.0000, -0.3795, 0.0002, 0
A, 221, GLY, 0.0000, -0.3795, 0.0002, 0
A, 222, HIS, 4.0934, 1.9022, 0.7509, 1
A, 223, SER, 0.0006, -0.3791, 0.0002, 0
A, 224, LEU, 0.0014, -0.3787, 0.0002, 0
A, 225, GLY, 0.0845, -0.3324, 0.0019, 0
A, 226, LEU, 1.0232, 0.1909, 0.1472, 1
A, 227, SER, 1.0418, 0.2012, 0.1521, 1
A, 228, HIS, 4.3482, 2.0442, 0.7745, 1
A, 229, SER, 0.3569, -0.1805, 0.0191, 0
A, 230, THR, 0.2870, -0.2195, 0.0129, 0
A, 231, ASP, 0.4405, -0.1339, 0.0283, 0
A, 232, ILE, 1.0044, 0.1804, 0.1421, 0
A, 233, GLY, 0.7892, 0.0604, 0.0887, 0
A, 234, ALA, 0.8689, 0.1049, 0.1075, 0
A, 235, LEU, 0.8973, 0.1207, 0.1145, 0
A, 236, MET, 0.1265, -0.3089, 0.0033, 0
A, 237, TYR, 1.2445, 0.3142, 0.2089, 0
A, 238, PRO, 2.5814, 1.0594, 0.5377, 1
A, 239, ASN, 0.8113, 0.0728, 0.0938, 1
A, 240, TYR, 1.0336, 0.1967, 0.1499, 1
A, 241, ILE, 1.0623, 0.2127, 0.1578, 0
A, 242, TYR, 0.4683, -0.1184, 0.0317, 0
A, 243, THR, 1.0067, 0.1817, 0.1427, 0
A, 244, GLY, 0.2077, -0.2637, 0.0073, 0
A, 245, ASP, 0.7730, 0.0514, 0.0852, 0
A, 246, VAL, 0.7015, 0.0116, 0.0700, 0
A, 247, GLN, 0.8216, 0.0785, 0.0962, 0
A, 248, LEU, 0.3612, -0.1781, 0.0195, 0
A, 249, SER, 0.3242, -0.1988, 0.0161, 0
A, 250, GLN, 0.0671, -0.3420, 0.0014, 0
A, 251, ASP, 0.5056, -0.0976, 0.0367, 0
A, 252, ASP, 0.0813, -0.3341, 0.0018, 0
A, 253, ILE, 0.1855, -0.2761, 0.0060, 0
A, 254, ASP, 0.1656, -0.2872, 0.0050, 0
A, 255, GLY, 0.0880, -0.3304, 0.0020, 0
A, 256, ILE, 0.0825, -0.3335, 0.0018, 0
A, 257, GLN, 0.0179, -0.3695, 0.0005, 0
A, 258, ALA, 0.0397, -0.3573, 0.0008, 0
A, 259, ILE, 0.0200, -0.3683, 0.0005, 0
A, 260, TYR, 0.0171, -0.3700, 0.0004, 0
A, 261, GLY, 0.0111, -0.3733, 0.0004, 0
A, 262, PRO, 0.0258, -0.3651, 0.0006, 0
A, 263, SER, 0.0373, -0.3587, 0.0008, 0
A, 264, GLU, 0.0438, -0.3550, 0.0009, 0
A, 265, ASN, 0.0210, -0.3677, 0.0005, 0
A, 266, PRO, 0.0279, -0.3639, 0.0006, 0
A, 267, VAL, 0.0102, -0.3738, 0.0004, 0
A, 268, GLN, 0.0415, -0.3563, 0.0008, 0
A, 269, PRO, 0.1411, -0.3008, 0.0039, 0
A, 270, SER, 0.1538, -0.2937, 0.0045, 0
A, 271, GLY, 0.1209, -0.3121, 0.0031, 0
A, 272, PRO, 0.0212, -0.3677, 0.0005, 0
A, 273, GLN, 0.3875, -0.1635, 0.0222, 0
A, 274, THR, 0.2083, -0.2634, 0.0073, 0
A, 275, PRO, 0.2263, -0.2533, 0.0085, 0
A, 276, GLN, 0.3368, -0.1917, 0.0173, 0
A, 277, VAL, 0.2312, -0.2506, 0.0088, 0
A, 278, CYS, 0.1749, -0.2820, 0.0055, 0
A, 279, ASP, 0.1950, -0.2708, 0.0066, 0
A, 280, SER, 0.1181, -0.3136, 0.0030, 0
A, 281, LYS, 0.0830, -0.3332, 0.0018, 0
A, 282, LEU, 0.1455, -0.2984, 0.0041, 0
A, 283, THR, 0.1634, -0.2884, 0.0049, 0
A, 284, PHE, 0.1181, -0.3137, 0.0030, 0
A, 285, ASP, 0.1488, -0.2965, 0.0043, 0
A, 286, ALA, 0.0377, -0.3585, 0.0008, 0
A, 287, ILE, 0.0131, -0.3722, 0.0004, 0
A, 288, THR, 0.0395, -0.3574, 0.0008, 0
A, 289, THR, 0.8047, 0.0691, 0.0923, 0
A, 290, LEU, 0.5340, -0.0818, 0.0409, 4
A, 291, ARG, 0.7860, 0.0587, 0.0880, 4
A, 292, GLY, 0.4034, -0.1546, 0.0239, 0
A, 293, GLU, 0.2966, -0.2142, 0.0137, 4
A, 294, LEU, 0.0003, -0.3793, 0.0002, 0
A, 295, MET, 0.0436, -0.3552, 0.0009, 0
A, 296, PHE, 0.0000, -0.3795, 0.0002, 0
A, 297, PHE, 0.0000, -0.3795, 0.0002, 0
A, 298, LYS, 0.1681, -0.2858, 0.0052, 0
A, 299, ASP, 0.1661, -0.2869, 0.0051, 0
A, 300, ARG, 0.8032, 0.0682, 0.0919, 0
A, 301, PHE, 0.2805, -0.2231, 0.0124, 0
A, 302, TYR, 0.0281, -0.3638, 0.0006, 0
A, 303, MET, 0.0273, -0.3642, 0.0006, 0
A, 304, ARG, 0.1791, -0.2796, 0.0057, 4
A, 305, THR, 0.0500, -0.3516, 0.0010, 0
A, 306, ASN, 0.4343, -0.1374, 0.0276, 0
A, 307, SER, 0.2484, -0.2410, 0.0100, 0
A, 308, PHE, 0.3544, -0.1819, 0.0189, 0
A, 309, TYR, 0.3266, -0.1974, 0.0163, 0
A, 310, PRO, 0.1885, -0.2744, 0.0062, 0
A, 311, GLU, 0.1706, -0.2844, 0.0053, 0
A, 312, VAL, 0.0868, -0.3311, 0.0019, 0
A, 313, GLU, 0.2440, -0.2435, 0.0097, 0
A, 314, LEU, 0.1932, -0.2718, 0.0065, 0
A, 315, ASN, 0.1979, -0.2691, 0.0067, 0
A, 316, PHE, 0.9436, 0.1465, 0.1262, 0
A, 317, ILE, 0.1205, -0.3123, 0.0031, 0
A, 318, SER, 0.1928, -0.2720, 0.0065, 0
A, 319, VAL, 0.2769, -0.2251, 0.0121, 0
A, 320, PHE, 0.3676, -0.1746, 0.0202, 4
A, 321, TRP, 0.4438, -0.1321, 0.0287, 4
A, 322, PRO, 0.0460, -0.3538, 0.0009, 0
A, 323, GLN, 0.0558, -0.3484, 0.0011, 0
A, 324, VAL, 0.0441, -0.3549, 0.0009, 0
A, 325, PRO, 0.0627, -0.3445, 0.0013, 0
A, 326, ASN, 0.1814, -0.2783, 0.0058, 0
A, 327, GLY, 0.0472, -0.3531, 0.0010, 0
A, 328, LEU, 0.0614, -0.3452, 0.0013, 0
A, 329, GLN, 0.0961, -0.3259, 0.0022, 0
A, 330, ALA, 0.0162, -0.3704, 0.0004, 0
A, 331, ALA, 0.0131, -0.3722, 0.0004, 0
A, 332, TYR, 0.0260, -0.3650, 0.0006, 0
A, 333, GLU, 0.8135, 0.0740, 0.0943, 0
A, 334, ILE, 0.7341, 0.0297, 0.0768, 0
A, 335, ALA, 0.7233, 0.0237, 0.0745, 0
A, 336, ASP, 0.2315, -0.2504, 0.0088, 0
A, 337, ARG, 0.2812, -0.2227, 0.0124, 2
A, 338, ASP, 0.0683, -0.3414, 0.0014, 0
A, 339, GLU, 0.6939, 0.0073, 0.0684, 2
A, 340, VAL, 0.3418, -0.1889, 0.0177, 4
A, 341, ARG, 0.7893, 0.0605, 0.0888, 2
A, 342, PHE, 0.0704, -0.3402, 0.0015, 0
A, 343, PHE, 0.0053, -0.3765, 0.0003, 0
A, 344, LYS, 0.0437, -0.3551, 0.0009, 0
A, 345, GLY, 0.0214, -0.3675, 0.0005, 0
A, 346, ASN, 0.0151, -0.3710, 0.0004, 0
A, 347, LYS, 0.0419, -0.3561, 0.0009, 0
A, 348, TYR, 0.8263, 0.0811, 0.0974, 2
A, 349, TRP, 0.0425, -0.3558, 0.0009, 0
A, 350, ALA, 0.5089, -0.0958, 0.0372, 0
A, 351, VAL, 0.3450, -0.1871, 0.0180, 0
A, 352, ARG, 0.3313, -0.1948, 0.0167, 0
A, 353, GLY, 0.4078, -0.1521, 0.0244, 4
A, 354, GLN, 0.4438, -0.1321, 0.0287, 4
A, 355, ASP, 0.0594, -0.3464, 0.0012, 0
A, 356, VAL, 0.0179, -0.3695, 0.0005, 0
A, 357, LEU, 0.0890, -0.3298, 0.0020, 2
A, 358, TYR, 0.1045, -0.3212, 0.0025, 0
A, 359, GLY, 0.0628, -0.3445, 0.0013, 0
A, 360, TYR, 0.8726, 0.1069, 0.1084, 2
A, 361, PRO, 0.0343, -0.3604, 0.0007, 0
A, 362, LYS, 0.6710, -0.0054, 0.0640, 2
A, 363, ASP, 0.0129, -0.3723, 0.0004, 0
A, 364, ILE, 0.0007, -0.3790, 0.0002, 0
A, 365, HIS, 0.0164, -0.3703, 0.0004, 0
A, 366, ARG, 0.1227, -0.3111, 0.0032, 2
A, 367, SER, 0.6973, 0.0092, 0.0691, 2
A, 368, PHE, 0.8040, 0.0687, 0.0921, 2
A, 369, GLY, 0.0778, -0.3361, 0.0017, 0
A, 370, PHE, 0.0657, -0.3428, 0.0014, 0
A, 371, PRO, 0.1676, -0.2860, 0.0051, 0
A, 372, SER, 0.0247, -0.3657, 0.0006, 0
A, 373, THR, 0.1715, -0.2839, 0.0053, 0
A, 374, VAL, 0.1353, -0.3040, 0.0037, 0
A, 375, LYS, 0.1006, -0.3234, 0.0024, 0
A, 376, ASN, 0.0426, -0.3557, 0.0009, 0
A, 377, ILE, 0.0465, -0.3536, 0.0009, 0
A, 378, ASP, 0.1268, -0.3088, 0.0033, 0
A, 379, ALA, 0.0195, -0.3686, 0.0005, 0
A, 380, ALA, 0.0184, -0.3692, 0.0005, 0
A, 381, VAL, 0.0349, -0.3600, 0.0007, 0
A, 382, PHE, 0.4664, -0.1195, 0.0314, 0
A, 383, GLU, 0.1765, -0.2811, 0.0056, 0
A, 384, GLU, 0.8039, 0.0687, 0.0921, 0
A, 385, ASP, 0.0373, -0.3587, 0.0008, 0
A, 386, THR, 0.2375, -0.2471, 0.0092, 0
A, 387, GLY, 0.0918, -0.3283, 0.0021, 0
A, 388, LYS, 0.2845, -0.2209, 0.0127, 0
A, 389, THR, 0.0000, -0.3795, 0.0002, 0
A, 390, TYR, 0.3821, -0.1665, 0.0216, 0
A, 391, PHE, 0.0000, -0.3795, 0.0002, 0
A, 392, PHE, 0.0023, -0.3782, 0.0003, 0
A, 393, VAL, 0.1649, -0.2875, 0.0050, 0
A, 394, ALA, 0.0816, -0.3340, 0.0018, 0
A, 395, HIS, 0.0868, -0.3311, 0.0019, 0
A, 396, GLU, 0.1756, -0.2816, 0.0055, 0
A, 397, CYS, 0.0509, -0.3511, 0.0010, 0
A, 398, TRP, 0.1954, -0.2705, 0.0066, 0
A, 399, ARG, 0.4237, -0.1433, 0.0263, 0
A, 400, TYR, 0.2847, -0.2208, 0.0127, 2
A, 401, ASP, 0.0555, -0.3485, 0.0011, 0
A, 402, GLU, 0.8097, 0.0719, 0.0934, 2
A, 403, TYR, 0.0641, -0.3437, 0.0013, 0
A, 404, LYS, 0.0135, -0.3719, 0.0004, 0
A, 405, GLN, 0.0524, -0.3503, 0.0011, 0
A, 406, SER, 0.0809, -0.3344, 0.0018, 0
A, 407, MET, 0.1097, -0.3183, 0.0027, 0
A, 408, ASP, 0.1959, -0.2702, 0.0066, 0
A, 409, THR, 0.0678, -0.3417, 0.0014, 0
A, 410, GLY, 0.0565, -0.3480, 0.0012, 0
A, 411, TYR, 0.3322, -0.1943, 0.0168, 0
A, 412, PRO, 0.1375, -0.3028, 0.0038, 0
A, 413, LYS, 0.2158, -0.2592, 0.0078, 0
A, 414, MET, 0.0409, -0.3566, 0.0008, 0
A, 415, ILE, 0.0148, -0.3712, 0.0004, 0
A, 416, ALA, 0.0330, -0.3611, 0.0007, 0
A, 417, GLU, 0.0264, -0.3648, 0.0006, 0
A, 418, GLU, 0.3283, -0.1965, 0.0164, 0
A, 419, PHE, 0.0555, -0.3485, 0.0011, 0
A, 420, PRO, 0.0226, -0.3669, 0.0005, 0
A, 421, GLY, 0.0633, -0.3442, 0.0013, 0
A, 422, ILE, 0.0625, -0.3447, 0.0013, 0
A, 423, GLY, 0.0630, -0.3443, 0.0013, 0
A, 424, ASN, 0.0676, -0.3418, 0.0014, 0
A, 425, LYS, 0.1803, -0.2790, 0.0058, 0
A, 426, VAL, 0.0831, -0.3332, 0.0018, 0
A, 427, ASP, 0.1773, -0.2807, 0.0056, 0
A, 428, ALA, 0.0393, -0.3576, 0.0008, 0
A, 429, VAL, 0.0184, -0.3692, 0.0005, 0
A, 430, PHE, 0.0287, -0.3634, 0.0006, 0
A, 431, GLN, 0.7617, 0.0451, 0.0826, 0
A, 432, LYS, 0.5886, -0.0514, 0.0495, 0
A, 433, ASP, 0.6096, -0.0397, 0.0529, 0
A, 434, GLY, 0.0381, -0.3582, 0.0008, 0
A, 435, PHE, 0.3123, -0.2054, 0.0150, 0
A, 436, LEU, 0.0028, -0.3779, 0.0003, 0
A, 437, TYR, 1.1919, 0.2849, 0.1939, 0
A, 438, PHE, 0.0129, -0.3723, 0.0004, 0
A, 439, PHE, 0.0129, -0.3723, 0.0004, 0
A, 440, HIS, 0.1039, -0.3216, 0.0025, 0
A, 441, GLY, 0.0762, -0.3370, 0.0016, 0
A, 442, THR, 0.0582, -0.3470, 0.0012, 0
A, 443, ARG, 0.0708, -0.3400, 0.0015, 0
A, 444, GLN, 0.9015, 0.1231, 0.1155, 0
A, 445, TYR, 0.2410, -0.2451, 0.0095, 0
A, 446, GLN, 0.8646, 0.1025, 0.1064, 0
A, 447, PHE, 0.0050, -0.3767, 0.0003, 0
A, 448, ASP, 0.0426, -0.3557, 0.0009, 0
A, 449, PHE, 0.4075, -0.1523, 0.0244, 0
A, 450, LYS, 0.0456, -0.3541, 0.0009, 0
A, 451, THR, 0.0140, -0.3716, 0.0004, 0
A, 452, LYS, 0.2891, -0.2183, 0.0131, 0
A, 453, ARG, 0.0130, -0.3722, 0.0004, 0
A, 454, ILE, 0.0434, -0.3553, 0.0009, 0
A, 455, LEU, 0.0502, -0.3515, 0.0010, 0
A, 456, THR, 0.6377, -0.0240, 0.0578, 0
A, 457, LEU, 0.1150, -0.3154, 0.0029, 0
A, 458, GLN, 0.9360, 0.1423, 0.1243, 0
A, 459, LYS, 0.3229, -0.1995, 0.0159, 0
A, 460, ALA, 0.0221, -0.3672, 0.0005, 0
A, 461, ASN, 0.1549, -0.2931, 0.0045, 0
A, 462, SER, 1.0288, 0.1940, 0.1487, 0
A, 463, TRP, 1.5100, 0.4622, 0.2855, 0
A, 464, PHE, 0.0896, -0.3295, 0.0020, 0
A, 465, ASN, 0.0767, -0.3367, 0.0016, 0
A, 466, CYS, 0.1336, -0.3050, 0.0036, 0
1 chain residue_label residue_name score zscore probability pocket
2 A 100 PHE 0.5863 -0.0527 0.0491 0
3 A 101 VAL 0.1968 -0.2697 0.0067 0
4 A 102 LEU 0.0989 -0.3243 0.0023 0
5 A 103 THR 0.6058 -0.0418 0.0523 1
6 A 104 PRO 0.0206 -0.3680 0.0005 0
7 A 105 GLY 0.0092 -0.3743 0.0003 0
8 A 106 ASN 0.0249 -0.3656 0.0006 0
9 A 107 PRO 0.0174 -0.3698 0.0005 0
10 A 108 ARG 0.0233 -0.3664 0.0005 0
11 A 109 TRP 0.0864 -0.3313 0.0019 0
12 A 110 GLU 0.0384 -0.3581 0.0008 0
13 A 111 ASN 0.0742 -0.3381 0.0016 0
14 A 112 THR 0.0271 -0.3643 0.0006 0
15 A 113 HIS 0.0742 -0.3381 0.0016 0
16 A 114 LEU 0.0632 -0.3442 0.0013 0
17 A 115 THR 0.0382 -0.3582 0.0008 0
18 A 116 TYR 0.0684 -0.3413 0.0014 0
19 A 117 ARG 0.0210 -0.3678 0.0005 0
20 A 118 ILE 0.0366 -0.3590 0.0008 0
21 A 119 GLU 1.0303 0.1948 0.1491 3
22 A 120 ASN 0.0779 -0.3360 0.0017 0
23 A 121 TYR 0.1071 -0.3197 0.0026 0
24 A 122 THR 0.0163 -0.3704 0.0004 0
25 A 123 PRO 0.0185 -0.3691 0.0005 0
26 A 124 ASP 0.0206 -0.3680 0.0005 0
27 A 125 LEU 0.1977 -0.2693 0.0067 0
28 A 126 SER 0.0248 -0.3656 0.0006 0
29 A 127 ARG 0.0981 -0.3248 0.0023 0
30 A 128 GLU 0.0397 -0.3573 0.0008 0
31 A 129 ASP 0.2691 -0.2295 0.0115 0
32 A 130 VAL 0.0862 -0.3314 0.0019 0
33 A 131 ASP 0.0672 -0.3420 0.0014 0
34 A 132 ARG 0.2657 -0.2313 0.0112 0
35 A 133 ALA 0.3319 -0.1945 0.0168 0
36 A 134 ILE 0.0525 -0.3502 0.0011 0
37 A 135 GLU 0.1450 -0.2986 0.0041 0
38 A 136 LYS 0.6173 -0.0354 0.0542 0
39 A 137 ALA 0.0002 -0.3794 0.0002 0
40 A 138 PHE 0.0770 -0.3366 0.0017 0
41 A 139 GLN 0.1328 -0.3054 0.0036 0
42 A 140 LEU 0.1585 -0.2911 0.0047 0
43 A 141 TRP 0.0676 -0.3418 0.0014 0
44 A 142 SER 0.1231 -0.3108 0.0032 0
45 A 143 ASN 0.1959 -0.2703 0.0066 0
46 A 144 VAL 0.1321 -0.3058 0.0035 0
47 A 145 SER 0.0061 -0.3760 0.0003 0
48 A 146 PRO 0.0286 -0.3635 0.0006 0
49 A 147 LEU 0.1067 -0.3200 0.0026 0
50 A 148 THR 0.1447 -0.2988 0.0041 0
51 A 149 PHE 0.1362 -0.3036 0.0037 0
52 A 150 THR 0.1135 -0.3162 0.0028 0
53 A 151 LYS 0.1105 -0.3179 0.0027 0
54 A 152 VAL 0.0485 -0.3524 0.0010 0
55 A 153 SER 0.0704 -0.3402 0.0015 0
56 A 154 GLU 0.0210 -0.3677 0.0005 0
57 A 155 GLY 0.0064 -0.3759 0.0003 0
58 A 156 GLN 0.0271 -0.3644 0.0006 3
59 A 157 ALA 0.0219 -0.3672 0.0005 0
60 A 158 ASP 0.0828 -0.3333 0.0018 0
61 A 159 ILE 0.0033 -0.3776 0.0003 0
62 A 160 MET 0.9464 0.1481 0.1269 3
63 A 161 ILE 0.7581 0.0431 0.0818 0
64 A 162 SER 1.0132 0.1853 0.1445 3
65 A 163 PHE 0.0534 -0.3497 0.0011 0
66 A 164 VAL 0.1232 -0.3108 0.0032 3
67 A 165 ARG 0.0402 -0.3570 0.0008 0
68 A 166 GLY 0.0114 -0.3731 0.0004 0
69 A 167 ASP 0.0143 -0.3715 0.0004 0
70 A 168 HIS 0.1673 -0.2862 0.0051 3
71 A 169 ARG 0.0373 -0.3586 0.0008 0
72 A 170 ASP 0.3326 -0.1941 0.0169 0
73 A 171 ASN 0.0857 -0.3317 0.0019 0
74 A 172 SER 0.2911 -0.2172 0.0133 0
75 A 173 PRO 0.0421 -0.3560 0.0009 0
76 A 174 PHE 0.0574 -0.3475 0.0012 0
77 A 175 ASP 0.0343 -0.3604 0.0007 0
78 A 176 GLY 0.0088 -0.3745 0.0003 0
79 A 177 PRO 0.0826 -0.3334 0.0018 0
80 A 178 GLY 0.2319 -0.2502 0.0089 0
81 A 179 GLY 0.2707 -0.2285 0.0116 0
82 A 180 ASN 1.6667 0.5495 0.3284 1
83 A 181 LEU 0.5081 -0.0963 0.0370 1
84 A 182 ALA 3.4334 1.5343 0.6739 1
85 A 183 HIS 3.4902 1.5660 0.6815 1
86 A 184 ALA 2.6624 1.1046 0.5529 1
87 A 185 PHE 0.9324 0.1403 0.1234 0
88 A 186 GLN 0.3475 -0.1858 0.0182 1
89 A 187 PRO 0.0494 -0.3519 0.0010 0
90 A 188 GLY 0.0776 -0.3362 0.0017 0
91 A 189 PRO 0.0802 -0.3348 0.0017 0
92 A 190 GLY 0.0561 -0.3482 0.0011 0
93 A 191 ILE 0.9980 0.1768 0.1404 3
94 A 192 GLY 0.0692 -0.3409 0.0015 0
95 A 193 GLY 0.0119 -0.3728 0.0004 0
96 A 194 ASP 0.9252 0.1363 0.1216 3
97 A 195 ALA 0.6133 -0.0376 0.0535 0
98 A 196 HIS 0.9880 0.1713 0.1377 3
99 A 197 PHE 0.0000 -0.3795 0.0002 0
100 A 198 ASP 0.0007 -0.3790 0.0002 0
101 A 199 GLU 0.0204 -0.3681 0.0005 0
102 A 200 ASP 0.0313 -0.3620 0.0007 0
103 A 201 GLU 0.0563 -0.3481 0.0012 0
104 A 202 ARG 0.1073 -0.3196 0.0026 0
105 A 203 TRP 0.0215 -0.3675 0.0005 0
106 A 204 THR 0.3933 -0.1603 0.0228 0
107 A 205 LYS 0.6021 -0.0438 0.0516 0
108 A 206 ASN 0.4865 -0.1083 0.0341 0
109 A 207 PHE 0.1933 -0.2717 0.0065 0
110 A 208 ARG 0.1135 -0.3162 0.0028 0
111 A 209 ASP 0.2679 -0.2302 0.0114 0
112 A 210 TYR 0.3235 -0.1992 0.0160 0
113 A 211 ASN 0.5608 -0.0668 0.0450 0
114 A 212 LEU 0.2492 -0.2405 0.0101 0
115 A 213 TYR 0.6073 -0.0410 0.0525 0
116 A 214 ARG 1.0201 0.1892 0.1464 1
117 A 215 VAL 1.1105 0.2395 0.1711 1
118 A 216 ALA 0.0158 -0.3706 0.0004 0
119 A 217 ALA 0.0000 -0.3795 0.0002 0
120 A 218 HIS 3.7453 1.7082 0.7135 1
121 A 219 GLU 3.7748 1.7246 0.7170 1
122 A 220 LEU 0.0000 -0.3795 0.0002 0
123 A 221 GLY 0.0000 -0.3795 0.0002 0
124 A 222 HIS 4.0934 1.9022 0.7509 1
125 A 223 SER 0.0006 -0.3791 0.0002 0
126 A 224 LEU 0.0014 -0.3787 0.0002 0
127 A 225 GLY 0.0845 -0.3324 0.0019 0
128 A 226 LEU 1.0232 0.1909 0.1472 1
129 A 227 SER 1.0418 0.2012 0.1521 1
130 A 228 HIS 4.3482 2.0442 0.7745 1
131 A 229 SER 0.3569 -0.1805 0.0191 0
132 A 230 THR 0.2870 -0.2195 0.0129 0
133 A 231 ASP 0.4405 -0.1339 0.0283 0
134 A 232 ILE 1.0044 0.1804 0.1421 0
135 A 233 GLY 0.7892 0.0604 0.0887 0
136 A 234 ALA 0.8689 0.1049 0.1075 0
137 A 235 LEU 0.8973 0.1207 0.1145 0
138 A 236 MET 0.1265 -0.3089 0.0033 0
139 A 237 TYR 1.2445 0.3142 0.2089 0
140 A 238 PRO 2.5814 1.0594 0.5377 1
141 A 239 ASN 0.8113 0.0728 0.0938 1
142 A 240 TYR 1.0336 0.1967 0.1499 1
143 A 241 ILE 1.0623 0.2127 0.1578 0
144 A 242 TYR 0.4683 -0.1184 0.0317 0
145 A 243 THR 1.0067 0.1817 0.1427 0
146 A 244 GLY 0.2077 -0.2637 0.0073 0
147 A 245 ASP 0.7730 0.0514 0.0852 0
148 A 246 VAL 0.7015 0.0116 0.0700 0
149 A 247 GLN 0.8216 0.0785 0.0962 0
150 A 248 LEU 0.3612 -0.1781 0.0195 0
151 A 249 SER 0.3242 -0.1988 0.0161 0
152 A 250 GLN 0.0671 -0.3420 0.0014 0
153 A 251 ASP 0.5056 -0.0976 0.0367 0
154 A 252 ASP 0.0813 -0.3341 0.0018 0
155 A 253 ILE 0.1855 -0.2761 0.0060 0
156 A 254 ASP 0.1656 -0.2872 0.0050 0
157 A 255 GLY 0.0880 -0.3304 0.0020 0
158 A 256 ILE 0.0825 -0.3335 0.0018 0
159 A 257 GLN 0.0179 -0.3695 0.0005 0
160 A 258 ALA 0.0397 -0.3573 0.0008 0
161 A 259 ILE 0.0200 -0.3683 0.0005 0
162 A 260 TYR 0.0171 -0.3700 0.0004 0
163 A 261 GLY 0.0111 -0.3733 0.0004 0
164 A 262 PRO 0.0258 -0.3651 0.0006 0
165 A 263 SER 0.0373 -0.3587 0.0008 0
166 A 264 GLU 0.0438 -0.3550 0.0009 0
167 A 265 ASN 0.0210 -0.3677 0.0005 0
168 A 266 PRO 0.0279 -0.3639 0.0006 0
169 A 267 VAL 0.0102 -0.3738 0.0004 0
170 A 268 GLN 0.0415 -0.3563 0.0008 0
171 A 269 PRO 0.1411 -0.3008 0.0039 0
172 A 270 SER 0.1538 -0.2937 0.0045 0
173 A 271 GLY 0.1209 -0.3121 0.0031 0
174 A 272 PRO 0.0212 -0.3677 0.0005 0
175 A 273 GLN 0.3875 -0.1635 0.0222 0
176 A 274 THR 0.2083 -0.2634 0.0073 0
177 A 275 PRO 0.2263 -0.2533 0.0085 0
178 A 276 GLN 0.3368 -0.1917 0.0173 0
179 A 277 VAL 0.2312 -0.2506 0.0088 0
180 A 278 CYS 0.1749 -0.2820 0.0055 0
181 A 279 ASP 0.1950 -0.2708 0.0066 0
182 A 280 SER 0.1181 -0.3136 0.0030 0
183 A 281 LYS 0.0830 -0.3332 0.0018 0
184 A 282 LEU 0.1455 -0.2984 0.0041 0
185 A 283 THR 0.1634 -0.2884 0.0049 0
186 A 284 PHE 0.1181 -0.3137 0.0030 0
187 A 285 ASP 0.1488 -0.2965 0.0043 0
188 A 286 ALA 0.0377 -0.3585 0.0008 0
189 A 287 ILE 0.0131 -0.3722 0.0004 0
190 A 288 THR 0.0395 -0.3574 0.0008 0
191 A 289 THR 0.8047 0.0691 0.0923 0
192 A 290 LEU 0.5340 -0.0818 0.0409 4
193 A 291 ARG 0.7860 0.0587 0.0880 4
194 A 292 GLY 0.4034 -0.1546 0.0239 0
195 A 293 GLU 0.2966 -0.2142 0.0137 4
196 A 294 LEU 0.0003 -0.3793 0.0002 0
197 A 295 MET 0.0436 -0.3552 0.0009 0
198 A 296 PHE 0.0000 -0.3795 0.0002 0
199 A 297 PHE 0.0000 -0.3795 0.0002 0
200 A 298 LYS 0.1681 -0.2858 0.0052 0
201 A 299 ASP 0.1661 -0.2869 0.0051 0
202 A 300 ARG 0.8032 0.0682 0.0919 0
203 A 301 PHE 0.2805 -0.2231 0.0124 0
204 A 302 TYR 0.0281 -0.3638 0.0006 0
205 A 303 MET 0.0273 -0.3642 0.0006 0
206 A 304 ARG 0.1791 -0.2796 0.0057 4
207 A 305 THR 0.0500 -0.3516 0.0010 0
208 A 306 ASN 0.4343 -0.1374 0.0276 0
209 A 307 SER 0.2484 -0.2410 0.0100 0
210 A 308 PHE 0.3544 -0.1819 0.0189 0
211 A 309 TYR 0.3266 -0.1974 0.0163 0
212 A 310 PRO 0.1885 -0.2744 0.0062 0
213 A 311 GLU 0.1706 -0.2844 0.0053 0
214 A 312 VAL 0.0868 -0.3311 0.0019 0
215 A 313 GLU 0.2440 -0.2435 0.0097 0
216 A 314 LEU 0.1932 -0.2718 0.0065 0
217 A 315 ASN 0.1979 -0.2691 0.0067 0
218 A 316 PHE 0.9436 0.1465 0.1262 0
219 A 317 ILE 0.1205 -0.3123 0.0031 0
220 A 318 SER 0.1928 -0.2720 0.0065 0
221 A 319 VAL 0.2769 -0.2251 0.0121 0
222 A 320 PHE 0.3676 -0.1746 0.0202 4
223 A 321 TRP 0.4438 -0.1321 0.0287 4
224 A 322 PRO 0.0460 -0.3538 0.0009 0
225 A 323 GLN 0.0558 -0.3484 0.0011 0
226 A 324 VAL 0.0441 -0.3549 0.0009 0
227 A 325 PRO 0.0627 -0.3445 0.0013 0
228 A 326 ASN 0.1814 -0.2783 0.0058 0
229 A 327 GLY 0.0472 -0.3531 0.0010 0
230 A 328 LEU 0.0614 -0.3452 0.0013 0
231 A 329 GLN 0.0961 -0.3259 0.0022 0
232 A 330 ALA 0.0162 -0.3704 0.0004 0
233 A 331 ALA 0.0131 -0.3722 0.0004 0
234 A 332 TYR 0.0260 -0.3650 0.0006 0
235 A 333 GLU 0.8135 0.0740 0.0943 0
236 A 334 ILE 0.7341 0.0297 0.0768 0
237 A 335 ALA 0.7233 0.0237 0.0745 0
238 A 336 ASP 0.2315 -0.2504 0.0088 0
239 A 337 ARG 0.2812 -0.2227 0.0124 2
240 A 338 ASP 0.0683 -0.3414 0.0014 0
241 A 339 GLU 0.6939 0.0073 0.0684 2
242 A 340 VAL 0.3418 -0.1889 0.0177 4
243 A 341 ARG 0.7893 0.0605 0.0888 2
244 A 342 PHE 0.0704 -0.3402 0.0015 0
245 A 343 PHE 0.0053 -0.3765 0.0003 0
246 A 344 LYS 0.0437 -0.3551 0.0009 0
247 A 345 GLY 0.0214 -0.3675 0.0005 0
248 A 346 ASN 0.0151 -0.3710 0.0004 0
249 A 347 LYS 0.0419 -0.3561 0.0009 0
250 A 348 TYR 0.8263 0.0811 0.0974 2
251 A 349 TRP 0.0425 -0.3558 0.0009 0
252 A 350 ALA 0.5089 -0.0958 0.0372 0
253 A 351 VAL 0.3450 -0.1871 0.0180 0
254 A 352 ARG 0.3313 -0.1948 0.0167 0
255 A 353 GLY 0.4078 -0.1521 0.0244 4
256 A 354 GLN 0.4438 -0.1321 0.0287 4
257 A 355 ASP 0.0594 -0.3464 0.0012 0
258 A 356 VAL 0.0179 -0.3695 0.0005 0
259 A 357 LEU 0.0890 -0.3298 0.0020 2
260 A 358 TYR 0.1045 -0.3212 0.0025 0
261 A 359 GLY 0.0628 -0.3445 0.0013 0
262 A 360 TYR 0.8726 0.1069 0.1084 2
263 A 361 PRO 0.0343 -0.3604 0.0007 0
264 A 362 LYS 0.6710 -0.0054 0.0640 2
265 A 363 ASP 0.0129 -0.3723 0.0004 0
266 A 364 ILE 0.0007 -0.3790 0.0002 0
267 A 365 HIS 0.0164 -0.3703 0.0004 0
268 A 366 ARG 0.1227 -0.3111 0.0032 2
269 A 367 SER 0.6973 0.0092 0.0691 2
270 A 368 PHE 0.8040 0.0687 0.0921 2
271 A 369 GLY 0.0778 -0.3361 0.0017 0
272 A 370 PHE 0.0657 -0.3428 0.0014 0
273 A 371 PRO 0.1676 -0.2860 0.0051 0
274 A 372 SER 0.0247 -0.3657 0.0006 0
275 A 373 THR 0.1715 -0.2839 0.0053 0
276 A 374 VAL 0.1353 -0.3040 0.0037 0
277 A 375 LYS 0.1006 -0.3234 0.0024 0
278 A 376 ASN 0.0426 -0.3557 0.0009 0
279 A 377 ILE 0.0465 -0.3536 0.0009 0
280 A 378 ASP 0.1268 -0.3088 0.0033 0
281 A 379 ALA 0.0195 -0.3686 0.0005 0
282 A 380 ALA 0.0184 -0.3692 0.0005 0
283 A 381 VAL 0.0349 -0.3600 0.0007 0
284 A 382 PHE 0.4664 -0.1195 0.0314 0
285 A 383 GLU 0.1765 -0.2811 0.0056 0
286 A 384 GLU 0.8039 0.0687 0.0921 0
287 A 385 ASP 0.0373 -0.3587 0.0008 0
288 A 386 THR 0.2375 -0.2471 0.0092 0
289 A 387 GLY 0.0918 -0.3283 0.0021 0
290 A 388 LYS 0.2845 -0.2209 0.0127 0
291 A 389 THR 0.0000 -0.3795 0.0002 0
292 A 390 TYR 0.3821 -0.1665 0.0216 0
293 A 391 PHE 0.0000 -0.3795 0.0002 0
294 A 392 PHE 0.0023 -0.3782 0.0003 0
295 A 393 VAL 0.1649 -0.2875 0.0050 0
296 A 394 ALA 0.0816 -0.3340 0.0018 0
297 A 395 HIS 0.0868 -0.3311 0.0019 0
298 A 396 GLU 0.1756 -0.2816 0.0055 0
299 A 397 CYS 0.0509 -0.3511 0.0010 0
300 A 398 TRP 0.1954 -0.2705 0.0066 0
301 A 399 ARG 0.4237 -0.1433 0.0263 0
302 A 400 TYR 0.2847 -0.2208 0.0127 2
303 A 401 ASP 0.0555 -0.3485 0.0011 0
304 A 402 GLU 0.8097 0.0719 0.0934 2
305 A 403 TYR 0.0641 -0.3437 0.0013 0
306 A 404 LYS 0.0135 -0.3719 0.0004 0
307 A 405 GLN 0.0524 -0.3503 0.0011 0
308 A 406 SER 0.0809 -0.3344 0.0018 0
309 A 407 MET 0.1097 -0.3183 0.0027 0
310 A 408 ASP 0.1959 -0.2702 0.0066 0
311 A 409 THR 0.0678 -0.3417 0.0014 0
312 A 410 GLY 0.0565 -0.3480 0.0012 0
313 A 411 TYR 0.3322 -0.1943 0.0168 0
314 A 412 PRO 0.1375 -0.3028 0.0038 0
315 A 413 LYS 0.2158 -0.2592 0.0078 0
316 A 414 MET 0.0409 -0.3566 0.0008 0
317 A 415 ILE 0.0148 -0.3712 0.0004 0
318 A 416 ALA 0.0330 -0.3611 0.0007 0
319 A 417 GLU 0.0264 -0.3648 0.0006 0
320 A 418 GLU 0.3283 -0.1965 0.0164 0
321 A 419 PHE 0.0555 -0.3485 0.0011 0
322 A 420 PRO 0.0226 -0.3669 0.0005 0
323 A 421 GLY 0.0633 -0.3442 0.0013 0
324 A 422 ILE 0.0625 -0.3447 0.0013 0
325 A 423 GLY 0.0630 -0.3443 0.0013 0
326 A 424 ASN 0.0676 -0.3418 0.0014 0
327 A 425 LYS 0.1803 -0.2790 0.0058 0
328 A 426 VAL 0.0831 -0.3332 0.0018 0
329 A 427 ASP 0.1773 -0.2807 0.0056 0
330 A 428 ALA 0.0393 -0.3576 0.0008 0
331 A 429 VAL 0.0184 -0.3692 0.0005 0
332 A 430 PHE 0.0287 -0.3634 0.0006 0
333 A 431 GLN 0.7617 0.0451 0.0826 0
334 A 432 LYS 0.5886 -0.0514 0.0495 0
335 A 433 ASP 0.6096 -0.0397 0.0529 0
336 A 434 GLY 0.0381 -0.3582 0.0008 0
337 A 435 PHE 0.3123 -0.2054 0.0150 0
338 A 436 LEU 0.0028 -0.3779 0.0003 0
339 A 437 TYR 1.1919 0.2849 0.1939 0
340 A 438 PHE 0.0129 -0.3723 0.0004 0
341 A 439 PHE 0.0129 -0.3723 0.0004 0
342 A 440 HIS 0.1039 -0.3216 0.0025 0
343 A 441 GLY 0.0762 -0.3370 0.0016 0
344 A 442 THR 0.0582 -0.3470 0.0012 0
345 A 443 ARG 0.0708 -0.3400 0.0015 0
346 A 444 GLN 0.9015 0.1231 0.1155 0
347 A 445 TYR 0.2410 -0.2451 0.0095 0
348 A 446 GLN 0.8646 0.1025 0.1064 0
349 A 447 PHE 0.0050 -0.3767 0.0003 0
350 A 448 ASP 0.0426 -0.3557 0.0009 0
351 A 449 PHE 0.4075 -0.1523 0.0244 0
352 A 450 LYS 0.0456 -0.3541 0.0009 0
353 A 451 THR 0.0140 -0.3716 0.0004 0
354 A 452 LYS 0.2891 -0.2183 0.0131 0
355 A 453 ARG 0.0130 -0.3722 0.0004 0
356 A 454 ILE 0.0434 -0.3553 0.0009 0
357 A 455 LEU 0.0502 -0.3515 0.0010 0
358 A 456 THR 0.6377 -0.0240 0.0578 0
359 A 457 LEU 0.1150 -0.3154 0.0029 0
360 A 458 GLN 0.9360 0.1423 0.1243 0
361 A 459 LYS 0.3229 -0.1995 0.0159 0
362 A 460 ALA 0.0221 -0.3672 0.0005 0
363 A 461 ASN 0.1549 -0.2931 0.0045 0
364 A 462 SER 1.0288 0.1940 0.1487 0
365 A 463 TRP 1.5100 0.4622 0.2855 0
366 A 464 PHE 0.0896 -0.3295 0.0020 0
367 A 465 ASN 0.0767 -0.3367 0.0016 0
368 A 466 CYS 0.1336 -0.3050 0.0036 0

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version: 2.6.0-dev.5
git head: 61b8863c
Params[
aa_mapping = minimal
apoholo_use_for_eval = false
apoholo_use_for_train = false
atom_table_feat_keep_sgn = false
atom_table_feat_pow = 2.0
atom_table_features = [apRawValids, apRawInvalids, atomicHydrophobicity]
average_feat_vectors = false
avg_pow = 1.0
avg_weighted = false
balance_class_weights = false
balance_density = false
balance_density_radius = 2.0
cache_datasets = false
chains = keep
check_vectors = false
classifier = FastRandomForest
classifier_train_stats = false
clear_prim_caches = false
clear_sec_caches = false
clustering_strategy = SingleLinkage
collect_eval_vectors = false
collect_negatives_from_true_pockets = false
collect_only_once = true
conserv_cloud_radius = 10.0
conservation_cache_dir = <null>
conservation_dirs = []
conservation_disable_cache = false
conservation_exponent = 1
conservation_provider = <null>
conservation_provider_threads = 0
conservation_provider_timeout = 600
conservation_provider_url = <null>
conservation_type = <null>
crossval_threads = 1
dataset_base_dir = /mnt/ssd/prank/p2rank-private/distro/test_data
deep_surrounding = false
delete_models = true
delete_vectors = true
electrostatics_dirs = []
energy_cloud_radius = 3.5
energy_cloud_radius2 = 6.0
energy_fallback_epsilon = 0.1
energy_fallback_sigma = 3.5
energy_min_r = 1.8
energy_missing_elem_policy = skip
energy_probe_epsilon = 0.12
energy_probe_sigma = 3.75
energy_rc = 9.0
energy_ron = 7.0
eval_tolerances = [0, 1, 2, 4, 10, 99]
export_points = true
export_points_format = csv
extended_pocket_cutoff = 3.5
extra_features = []
extra_output = []
fail_fast = false
fail_on_conserv_seq_mismatch = false
false_positive_cost = 2.0
feat_aa_properties = []
feat_asa_neigh_radius = 6.0
feat_asa_probe_radius = 1.4
feat_asa_probe_radius2 = 3.0
feat_crang_contact_dist = 4.0
feat_csv_columns = []
feat_csv_directories = []
feat_csv_ignore_missing = false
feat_pmass_natoms = 70
feat_pmass_nsasp = 40
feat_pmass_radius = 11.0
feat_propensity_tables = SprintT1070
feat_stmotif_motifs = [C2H2, C4, C3H1, E1H2, C2H1, H3, D1H2, C3, D1H1, E1H1, C1H3, C2, H2]
feat_stmotif_radius = 4.0
feat_stmotif_useradius = true
feature_filters = []
feature_importances = false
features = [chem, volsite, protrusion, bfactor]
folds = 5
fpocket_command = fpocket
fpocket_keep_output = true
grid_cell_edge = 2.0
grid_cutoff_radius = 3.4
hopt_cache_labeled_points = false
hopt_max_iterations = 1000
hopt_objective = DCA_4_0
hopt_optimizer = spearmint
hopt_python_command = python
hopt_spearmint_dir =
hopt_train_only_once = false
identify_peptides_by_labeling = false
ignore_het_groups = [HOH, DOD, WAT, NAG, MAN, UNK, GLC, ABA, MPD, GOL, SO4, PO4]
inner_classifier = FastRandomForest
installDir = /mnt/ssd/prank/p2rank-private/distro
kdtree_implementation = AtomKdTreeV2
label_residues = true
ligand_clustering_distance = 1.7
ligand_derived_point_labeling = true
ligand_induced_volume_cutoff = 2.5
ligand_protein_contact_distance = 4.0
ligc_prot_dist = 5.5
load_conservation = false
loaded_pockets_limit = 0
log_cases = true
log_level = INFO
log_scores_to_file =
log_to_console = true
log_to_file = true
loop = 1
max_train_instances = 0
meta_classifier_iterations = 5
min_ligand_atoms = 5
model = default
neighbourhood_radius = 6.0
neutral_points_margin = 5.5
out_file = <null>
out_format = keep
out_prefix_date = false
out_subdir = <null>
output_base_dir = /mnt/ssd/prank/p2rank-private/distro/test_output
output_only_stats = false
pair_hist_bins = 5
pair_hist_deep = true
pair_hist_normalize = false
pair_hist_radius = 6.0
pair_hist_smooth = false
pair_hist_subsample_limit = 0
parallel = true
plb_rescorer_atomic = false
ploop_delete_runs = false
ploop_fixed_subfeatures = []
ploop_zip_runs = false
point_max_distfrom_pocket = 4.5
point_min_distfrom_protein = 2.5
point_sampler = SurfacePointSampler
point_sampling_strategy = surface
point_score_pow = 2.0
positive_def_ligtypes = [relevant]
positive_point_ligand_distance = 2.6
pred_clustering_dist = 3.0
pred_min_cluster_size = 3
pred_point_threshold = 0.35
pred_protein_surface_cutoff = 3.5
predict_residues = false
predictions = true
probatp_res_transformer = {models_dir}/_score_transform/residue/default_ProbabilityScoreTransformer.json
probatp_transformer = {models_dir}/_score_transform/default_ProbabilityScoreTransformer.json
protr_hist_bins = 5
protr_hist_cumulative = false
protr_hist_relative = false
protrusion_radius = 10.0
r_generate_plots = true
r_plot_stddevs = false
r_threads = 16
randomize_seed = false
rescorer = ModelBasedRescorer
residue_point_score_pow = -1.0
residue_score_extra_dist = 2.0
residue_score_only_exposed = false
residue_score_sum_to_avg = 0.0
residue_score_threshold = 1.0
residue_score_transform = NONE
residue_table_features = []
rf_bagsize = 100
rf_batch_prediction = true
rf_depth = 0
rf_ensure_leaves_normalized = false
rf_features = 0
rf_flatten = false
rf_flatten_as_legacy = true
rf_flatten_target = LegacyFlatBinaryForest
rf_threads = 16
rf_trees = 100
sample_negatives_from_decoys = false
sampling_multiplier = 3
score_pockets_by = p2rank
score_point_limit = 0
seed = 42
selected_stats = [DCA_4_0, DCA_4_2, DCA_4_4, DCC_10_0, DCC_10_2, DSOR_02_0, DSOR_02_2, DSWO_05_0, DSWO_05_2, point_MCC, point_TPX, point_LOG_LOSS, AVG_DSO_SUCC, AVG_LIGCOV_SUCC, AVG_POCKETS, AVG_POCKET_SAS_POINTS, AVG_POCKET_SAS_POINTS_TRUE_POCKETS, TIME_TRAINEVAL_AVG_M]
site_centroid_method = atoms_center_of_mass
site_eval_sas_pts_as_atoms = false
smooth_representation = false
smoothing_radius = 4.5
solvent_radius = 1.6
ss_cloud_radius = 10.0
stats_collect_predictions = true
stats_curves = false
stdout_timestamp =
strict_inner_points = false
subsampl_high_protrusion_negatives = false
subsample = false
supersample = false
surface_additional_cutoff = 2.5
surface_sparsify = true
target_class_ratio = 0.1
target_class_weight_ratio = 0.1
tessellation = 2
threads = 16
train_lig_cutoff = 0.0
train_pockets = 9
train_protein_limit = 0
train_random_rotated_copies = 0
train_score_transformers = []
train_score_transformers_for_residues = false
train_tessellation = 2
train_tessellation_negatives = 2
use_kdtree_cutout_sphere_thrashold = 150
use_only_positive_score = true
use_optimized_surface = true
vis_all_surface = false
vis_copy_proteins = true
vis_generate_proteins = true
vis_highlight_ligands = false
vis_point_gradient_max = 0.7
vis_point_gradient_pymol = green_red
vis_renderers = [pymol, chimerax]
vis_site_centers = false
visualizations = true
weight_dist_param = 4.5
weight_function = INV
weight_power = 2.0
weight_sigma = 2.2
xenergy_cloud2_layered = true
xenergy_cloud_stdev_type = 0
xenergy_solvent_radius = 1.6
xenergy_tessellation = 2
xpoint_zscore_threshold = 0.0
zip_log_file = false
zip_visualizations = false
zscoretp_res_transformer = {models_dir}/_score_transform/residue/default_ZscoreTpTransformer.json
zscoretp_transformer = {models_dir}/_score_transform/default_ZscoreTpTransformer.json
]

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open data/1fbl.cif
surf
hide solvent
color protein #bdbdde
color ligand magenta
color name color_pocket1 #5c93e6
color name color_pocket2 #7d47b3
color name color_pocket3 #e65cae
color name color_pocket4 #b36847
name pocket1_atoms @@serial_number=700 @@serial_number=692 @@serial_number=664 @@serial_number=670 @@serial_number=942 @@serial_number=33 @@serial_number=679 @@serial_number=1016 @@serial_number=32 @@serial_number=1026 @@serial_number=991 @@serial_number=958 @@serial_number=676 @@serial_number=960 @@serial_number=989 @@serial_number=959 @@serial_number=992 @@serial_number=971 @@serial_number=963 @@serial_number=994 @@serial_number=961 @@serial_number=972 @@serial_number=993 @@serial_number=962 @@serial_number=1036 @@serial_number=1035 @@serial_number=1033 @@serial_number=651 @@serial_number=1106 @@serial_number=658 @@serial_number=659 @@serial_number=1112 @@serial_number=1118 @@serial_number=943 @@serial_number=938 @@serial_number=929 @@serial_number=934 @@serial_number=1124 @@serial_number=1119 @@serial_number=1122
color pocket1_atoms color_pocket1
name pocket2_atoms @@serial_number=2064 @@serial_number=2091 @@serial_number=2092 @@serial_number=2109 @@serial_number=2144 @@serial_number=1991 @@serial_number=2151 @@serial_number=2163 @@serial_number=2426 @@serial_number=2161 @@serial_number=1926 @@serial_number=1910 @@serial_number=2439 @@serial_number=2444 @@serial_number=1909 @@serial_number=1891 @@serial_number=1890 @@serial_number=2150
color pocket2_atoms color_pocket2
name pocket3_atoms @@serial_number=472 @@serial_number=515 @@serial_number=761 @@serial_number=501 @@serial_number=171 @@serial_number=172 @@serial_number=173 @@serial_number=514 @@serial_number=499 @@serial_number=728 @@serial_number=730 @@serial_number=746 @@serial_number=560 @@serial_number=532 @@serial_number=760
color pocket3_atoms color_pocket3
name pocket4_atoms @@serial_number=1766 @@serial_number=1769 @@serial_number=1756 @@serial_number=1757 @@serial_number=2035 @@serial_number=1499 @@serial_number=2034 @@serial_number=2030 @@serial_number=2031 @@serial_number=1619 @@serial_number=1513 @@serial_number=1489 @@serial_number=1490 @@serial_number=1488 @@serial_number=1620 @@serial_number=1497 @@serial_number=1917
color pocket4_atoms color_pocket4
open data/1fbl.cif_points.pdb.gz
color by bfactor #2 palette lime:red range 0,0.7
set bgcolor #242455
transparency 35
graphics silhouettes true
lighting full
view

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from pymol import cmd,stored
set depth_cue, 1
set fog_start, 0.4
set_color b_col, [36,36,85]
set_color t_col, [10,10,10]
set bg_rgb_bottom, b_col
set bg_rgb_top, t_col
set bg_gradient
set spec_power = 200
set spec_refl = 0
load "data/1fbl.cif", protein
create ligands, protein and organic
select xlig, protein and organic
delete xlig
hide everything, all
color white, elem c
color bluewhite, protein
#show_as cartoon, protein
show surface, protein
#set transparency, 0.15
show sticks, ligands
set stick_color, magenta
# SAS points
load "data/1fbl.cif_points.pdb.gz", points
hide nonbonded, points
show nb_spheres, points
set sphere_scale, 0.2, points
cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
stored.list=[]
cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP
lastSTP=stored.list[-1] # get the index of the last residue
hide lines, resn STP
cmd.select("rest", "resn STP and resi 0")
for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
set_color pcol1 = [0.361,0.576,0.902]
select surf_pocket1, protein and id [700,692,664,670,942,33,679,1016,32,1026,991,958,676,960,989,959,992,971,963,994,961,972,993,962,1036,1035,1033,651,1106,658,659,1112,1118,943,938,929,934,1124,1119,1122]
set surface_color, pcol1, surf_pocket1
set_color pcol2 = [0.490,0.278,0.702]
select surf_pocket2, protein and id [2064,2091,2092,2109,2144,1991,2151,2163,2426,2161,1926,1910,2439,2444,1909,1891,1890,2150]
set surface_color, pcol2, surf_pocket2
set_color pcol3 = [0.902,0.361,0.682]
select surf_pocket3, protein and id [472,515,761,501,171,172,173,514,499,728,730,746,560,532,760]
set surface_color, pcol3, surf_pocket3
set_color pcol4 = [0.702,0.408,0.278]
select surf_pocket4, protein and id [1766,1769,1756,1757,2035,1499,2034,2030,2031,1619,1513,1489,1490,1488,1620,1497,1917]
set surface_color, pcol4, surf_pocket4
deselect
orient

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# P2Rank Notebooks
Example Jupyter notebooks for working with P2Rank output.
## Notebooks
- **analyze_p2rank_output.ipynb** - Load and explore `_predictions.csv` and `_residues.csv` output files using pandas.
## Requirements
```bash
pip install pandas matplotlib jupyter
```
## Running
```bash
cd documentation/notebooks
jupyter notebook
```
Then open `analyze_p2rank_output.ipynb`.
The notebook uses example output in `p2rank_output/predict_1fbl/` which is included in this directory.