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SeRenDIP Resultsnew job |
In the table below you can see the SeRenDIP example pdb 1YVB chain A Plasmodium falciparum Cysteine Protease . The table contains sequence position, prediction scores and classification based on the default cut-off of 0.5 (above is predicted interaction).
Download raw dataYou can download the output file and the full feature table.
Please cite:
- Qingzhen Hou1, Reza Haydarlou, Bas Stringer, Katharina Waury, Henriette Capel, Sanne Abeln, Jaap Heringa, K. Anton Feenstra SeRenDIP-CE: Sequence-based Interface Prediction for Conformational Epitopes Bioinformatics 37, pp 3421–3427, 2021, doi: 10.1093/bioinformatics/btab321
1Department of Biostatistics, School of Public Health & National institute of health data science of China; Shandong 250002, P. R. China- Qingzhen Hou1, Paul De Geest, Christian Griffioen, Sanne Abeln, Jaap Heringa, K. Anton Feenstra. SeRenDIP: remastered alignment profiles for fast and accurate predictions of PPI interface positions. Bioinformatics 35, pp 4794–4796, 2019, doi: 10.1093/bioinformatics/btz428
13BIO-BioInfo – BioModeling, BioInformatics & BioProcesses, Université Libre de Bruxelles- Qingzhen Hou, Paul De Geest, Wim F. Vranken, Jaap Heringa and K. Anton Feenstra
Seeing the Trees through the Forest: Sequence-based Homo- and Heteromeric Protein-protein Interaction sites prediction using Random Forest. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx005
Color better than threshold:
Sequence Heteromeric Prediction Pos AA Model Pred x of 233 rows match filter(s) 5 E 0.470 NI 6 E 0.442 NI 7 V 0.370 NI 8 I 0.382 NI 9 K 0.450 NI 10 K 0.432 NI 11 Y 0.430 NI 12 R 0.468 NI 13 G 0.388 NI 14 E 0.472 NI 15 E 0.450 NI 16 N 0.444 NI 17 F 0.458 NI 18 D 0.432 NI 19 H 0.462 NI 20 A 0.486 NI 21 A 0.562 I 22 Y 0.510 I 23 D 0.516 I 24 W 0.378 NI 25 R 0.516 I 26 L 0.492 NI 27 H 0.474 NI 28 S 0.462 NI 29 G 0.484 NI 30 V 0.456 NI 31 T 0.438 NI 32 P 0.490 NI 33 V 0.250 NI 34 K 0.524 I 35 D 0.648 I 36 Q 0.530 I 37 K 0.602 I 38 N 0.694 I 39 C 0.502 I 40 G 0.514 I 41 S 0.414 NI 42 C 0.402 NI 43 W 0.434 NI 44 A 0.184 NI 45 F 0.278 NI 46 S 0.140 NI 47 S 0.214 NI 48 I 0.176 NI 49 G 0.198 NI 50 S 0.272 NI 51 V 0.188 NI 52 E 0.250 NI 53 S 0.204 NI 54 Q 0.484 NI 55 Y 0.462 NI 56 A 0.408 NI 57 I 0.518 I 58 R 0.580 I 59 K 0.550 I 60 N 0.548 I 61 K 0.532 I 62 L 0.518 I 63 I 0.518 I 64 T 0.514 I 65 L 0.348 NI 66 S 0.386 NI 67 E 0.578 I 68 Q 0.532 I 69 E 0.550 I 70 L 0.368 NI 71 V 0.418 NI 72 D 0.398 NI 73 C 0.336 NI 74 S 0.452 NI 75 F 0.556 I 76 K 0.542 I 77 N 0.502 I 78 Y 0.562 I 79 G 0.424 NI 80 C 0.488 NI 81 N 0.576 I 82 G 0.554 I 83 G 0.572 I 84 L 0.648 I 85 I 0.592 I 86 N 0.570 I 87 N 0.554 I 88 A 0.152 NI 89 F 0.240 NI 90 E 0.512 I 91 D 0.498 NI 92 M 0.276 NI 93 I 0.444 NI 94 E 0.514 I 95 L 0.448 NI 96 G 0.436 NI 97 G 0.422 NI 98 I 0.424 NI 99 C 0.454 NI 100 P 0.444 NI 101 D 0.478 NI 102 G 0.522 I 103 D 0.500 NI 104 Y 0.444 NI 105 P 0.448 NI 106 Y 0.422 NI 107 V 0.476 NI 108 S 0.496 NI 109 D 0.430 NI 110 A 0.536 I 111 P 0.586 I 112 N 0.454 NI 113 L 0.486 NI 114 C 0.280 NI 115 N 0.432 NI 116 I 0.408 NI 117 D 0.478 NI 118 R 0.466 NI 119 C 0.386 NI 120 T 0.422 NI 121 E 0.410 NI 122 K 0.458 NI 123 Y 0.316 NI 124 G 0.430 NI 125 I 0.320 NI 126 K 0.492 NI 127 N 0.528 I 128 Y 0.510 I 129 L 0.452 NI 130 S 0.468 NI 131 V 0.430 NI 132 P 0.452 NI 133 D 0.462 NI 134 N 0.402 NI 135 K 0.392 NI 136 L 0.164 NI 137 K 0.332 NI 138 E 0.350 NI 139 A 0.464 NI 140 L 0.166 NI 141 R 0.456 NI 142 F 0.450 NI 143 L 0.424 NI 144 G 0.340 NI 145 P 0.364 NI 146 I 0.278 NI 147 S 0.192 NI 148 I 0.128 NI 149 S 0.140 NI 150 V 0.204 NI 151 A 0.442 NI 152 V 0.404 NI 153 S 0.538 I 154 D 0.634 I 155 D 0.556 I 156 F 0.406 NI 157 A 0.590 I 158 F 0.612 I 159 Y 0.342 NI 160 K 0.652 I 161 E 0.594 I 162 G 0.372 NI 163 I 0.402 NI 164 F 0.390 NI 165 D 0.408 NI 166 G 0.502 I 167 E 0.520 I 168 C 0.478 NI 169 G 0.480 NI 170 D 0.528 I 171 Q 0.514 I 172 L 0.478 NI 173 N 0.522 I 174 H 0.480 NI 175 A 0.398 NI 176 V 0.100 NI 177 M 0.168 NI 178 L 0.104 NI 179 V 0.248 NI 180 G 0.298 NI 181 F 0.380 NI 182 G 0.494 NI 183 M 0.504 I 184 K 0.566 I 185 E 0.530 I 186 I 0.580 I 187 V 0.472 NI 188 N 0.528 I 189 P 0.484 NI 190 L 0.528 I 191 T 0.516 I 192 K 0.480 NI 193 K 0.494 NI 194 G 0.478 NI 195 E 0.456 NI 196 K 0.472 NI 197 H 0.472 NI 198 Y 0.468 NI 199 Y 0.454 NI 200 Y 0.254 NI 201 I 0.250 NI 202 I 0.132 NI 203 K 0.344 NI 204 N 0.366 NI 205 S 0.492 NI 206 W 0.630 I 207 G 0.524 I 208 Q 0.602 I 209 Q 0.680 I 210 W 0.596 I 211 G 0.536 I 212 E 0.430 NI 213 R 0.494 NI 214 G 0.324 NI 215 F 0.392 NI 216 I 0.102 NI 217 N 0.396 NI 218 I 0.150 NI 219 E 0.500 NI 220 T 0.544 I 221 D 0.530 I 222 E 0.544 I 223 S 0.522 I 224 G 0.534 I 225 L 0.560 I 226 M 0.566 I 227 R 0.474 NI 228 K 0.500 NI 229 C 0.354 NI 230 G 0.324 NI 231 L 0.318 NI 232 G 0.420 NI 233 T 0.450 NI 234 D 0.564 I 235 A 0.406 NI 236 F 0.516 I 237 I 0.470 NI
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