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SeRenDIP-CE Conformational Epitope prediction Resultsnew job |
In the table below you can see the SeRenDIP-CE Conformational Epitope prediction example P0DTD2 — Name: SARS-CoV-2 Protein 9b — UniProtKB: ORF9B_SARS2 . 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 advance 11 May 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 Models Epitope Prediction Pos AA Model 1 Model 2 Model 3 Model 4 Model 5 Average Pred Std. Dev. Z-score x of 89 rows match filter(s) 5 I 0.664 0.576 0.612 0.632 0.606 0.618 I 0.0326 -0.2267 6 S 0.680 0.634 0.626 0.666 0.588 0.639 I 0.0361 0.2809 7 E 0.704 0.582 0.598 0.690 0.608 0.636 I 0.0563 0.2224 8 M 0.644 0.614 0.560 0.660 0.616 0.619 I 0.0381 -0.2072 9 H 0.590 0.612 0.600 0.638 0.598 0.608 I 0.0187 -0.4806 10 P 0.652 0.598 0.642 0.672 0.598 0.632 I 0.0332 0.1247 11 A 0.682 0.642 0.614 0.762 0.680 0.676 I 0.0558 1.1889 12 L 0.662 0.608 0.632 0.740 0.666 0.662 I 0.0498 0.8374 13 R 0.692 0.620 0.664 0.792 0.664 0.686 I 0.0644 1.4427 14 L 0.666 0.600 0.642 0.764 0.682 0.671 I 0.0606 1.0620 15 V 0.632 0.608 0.622 0.774 0.644 0.656 I 0.0673 0.7007 16 D 0.616 0.682 0.666 0.738 0.650 0.670 I 0.0450 1.0522 17 P 0.598 0.664 0.682 0.740 0.684 0.674 I 0.0510 1.1303 18 Q 0.532 0.622 0.692 0.762 0.626 0.647 I 0.0859 0.4762 19 I 0.538 0.620 0.556 0.664 0.640 0.604 I 0.0543 -0.5782 20 Q 0.516 0.634 0.650 0.758 0.568 0.625 I 0.0915 -0.0510 21 L 0.464 0.622 0.532 0.680 0.582 0.576 I 0.0828 -1.2519 22 A 0.512 0.592 0.616 0.732 0.616 0.614 I 0.0788 -0.3341 23 V 0.520 0.596 0.598 0.658 0.566 0.588 I 0.0504 -0.9687 24 T 0.608 0.640 0.630 0.698 0.612 0.638 I 0.0362 0.2516 25 R 0.640 0.646 0.672 0.702 0.670 0.666 I 0.0246 0.9448 26 M 0.556 0.582 0.620 0.686 0.622 0.613 I 0.0492 -0.3439 27 E 0.636 0.698 0.700 0.740 0.664 0.688 I 0.0395 1.4720 28 N 0.692 0.676 0.658 0.750 0.680 0.691 I 0.0351 1.5599 29 A 0.580 0.586 0.576 0.646 0.652 0.608 I 0.0377 -0.4708 30 V 0.656 0.586 0.606 0.720 0.600 0.634 I 0.0551 0.1540 31 G 0.642 0.586 0.564 0.710 0.668 0.634 I 0.0596 0.1638 32 R 0.706 0.614 0.692 0.740 0.688 0.688 I 0.0462 1.4818 33 D 0.690 0.618 0.632 0.660 0.690 0.658 I 0.0329 0.7496 34 Q 0.642 0.628 0.604 0.700 0.686 0.652 I 0.0401 0.6031 35 N 0.708 0.626 0.660 0.704 0.730 0.686 I 0.0419 1.4232 36 N 0.656 0.642 0.650 0.672 0.710 0.666 I 0.0269 0.9448 37 V 0.616 0.642 0.620 0.690 0.672 0.648 I 0.0323 0.5055 38 G 0.596 0.604 0.618 0.662 0.640 0.624 I 0.0270 -0.0803 39 P 0.574 0.626 0.604 0.644 0.626 0.615 I 0.0269 -0.3048 40 K 0.570 0.614 0.626 0.656 0.604 0.614 I 0.0314 -0.3244 41 V 0.506 0.624 0.562 0.594 0.640 0.585 I 0.0534 -1.0273 42 Y 0.476 0.580 0.568 0.598 0.546 0.554 I 0.0473 -1.7986 43 P 0.516 0.620 0.582 0.580 0.594 0.578 I 0.0384 -1.1933 44 I 0.470 0.606 0.668 0.564 0.540 0.570 I 0.0739 -1.4081 45 I 0.500 0.512 0.624 0.624 0.562 0.564 I 0.0592 -1.5350 46 L 0.486 0.466 0.570 0.614 0.550 0.537 I 0.0609 -2.1989 47 R 0.618 0.670 0.606 0.672 0.652 0.644 I 0.0302 0.3981 48 L 0.546 0.524 0.554 0.654 0.558 0.567 I 0.0503 -1.4667 49 G 0.564 0.628 0.670 0.708 0.604 0.635 I 0.0561 0.1833 50 S 0.608 0.688 0.644 0.740 0.692 0.674 I 0.0503 1.1498 51 P 0.584 0.744 0.678 0.724 0.672 0.680 I 0.0619 1.2963 52 L 0.566 0.704 0.606 0.660 0.644 0.636 I 0.0526 0.2126 53 S 0.544 0.600 0.552 0.662 0.584 0.588 I 0.0471 -0.9492 54 L 0.574 0.592 0.584 0.640 0.616 0.601 I 0.0267 -0.6368 55 N 0.646 0.638 0.558 0.684 0.572 0.620 I 0.0530 -0.1877 56 M 0.550 0.604 0.584 0.684 0.668 0.618 I 0.0566 -0.2267 57 A 0.564 0.542 0.616 0.736 0.626 0.617 I 0.0753 -0.2560 58 R 0.652 0.642 0.610 0.724 0.628 0.651 I 0.0436 0.5836 59 K 0.688 0.604 0.622 0.706 0.628 0.650 I 0.0446 0.5445 60 T 0.622 0.604 0.626 0.654 0.600 0.621 I 0.0215 -0.1486 61 L 0.572 0.578 0.596 0.664 0.570 0.596 I 0.0394 -0.7637 62 N 0.640 0.618 0.598 0.680 0.606 0.628 I 0.0329 0.0271 63 S 0.586 0.586 0.592 0.610 0.580 0.591 I 0.0115 -0.8906 64 L 0.574 0.642 0.576 0.668 0.602 0.612 I 0.0415 -0.3634 65 E 0.628 0.586 0.620 0.642 0.576 0.610 I 0.0282 -0.4122 66 D 0.628 0.606 0.632 0.668 0.602 0.627 I 0.0263 -0.0022 67 K 0.670 0.618 0.640 0.692 0.626 0.649 I 0.0311 0.5348 68 A 0.592 0.612 0.588 0.682 0.592 0.613 I 0.0396 -0.3439 69 F 0.546 0.552 0.558 0.662 0.584 0.580 I 0.0479 -1.1445 70 Q 0.580 0.626 0.614 0.658 0.650 0.626 I 0.0311 -0.0412 71 L 0.574 0.616 0.632 0.652 0.628 0.620 I 0.0290 -0.1682 72 T 0.512 0.560 0.570 0.584 0.612 0.568 I 0.0367 -1.4569 73 P 0.560 0.640 0.628 0.690 0.624 0.628 I 0.0464 0.0271 74 I 0.462 0.638 0.590 0.586 0.604 0.576 I 0.0669 -1.2519 75 A 0.582 0.608 0.596 0.610 0.606 0.600 I 0.0116 -0.6563 76 V 0.550 0.606 0.636 0.604 0.578 0.595 I 0.0324 -0.7930 77 Q 0.618 0.666 0.658 0.730 0.684 0.671 I 0.0408 1.0717 78 M 0.456 0.598 0.600 0.642 0.568 0.573 I 0.0704 -1.3300 79 T 0.562 0.614 0.642 0.704 0.612 0.627 I 0.0519 -0.0120 80 K 0.656 0.696 0.730 0.772 0.696 0.710 I 0.0435 2.0188 81 L 0.598 0.632 0.646 0.722 0.650 0.650 I 0.0454 0.5445 82 A 0.612 0.594 0.592 0.674 0.660 0.626 I 0.0382 -0.0217 83 T 0.704 0.618 0.708 0.768 0.722 0.704 I 0.0544 1.8723 84 T 0.676 0.594 0.644 0.734 0.670 0.664 I 0.0509 0.8862 85 E 0.676 0.722 0.680 0.782 0.674 0.707 I 0.0464 1.9407 86 E 0.674 0.688 0.778 0.818 0.732 0.738 I 0.0605 2.7022 87 L 0.604 0.642 0.614 0.686 0.710 0.651 I 0.0457 0.5836 88 P 0.518 0.558 0.612 0.570 0.606 0.573 I 0.0383 -1.3300 89 D 0.616 0.636 0.632 0.586 0.612 0.616 I 0.0198 -0.2658 90 E 0.568 0.614 0.634 0.614 0.578 0.602 I 0.0276 -0.6270 91 F 0.490 0.598 0.528 0.598 0.638 0.570 I 0.0599 -1.3885 92 V 0.534 0.552 0.528 0.604 0.612 0.566 I 0.0394 -1.4959 93 V 0.548 0.514 0.530 0.594 0.554 0.548 I 0.0301 -1.9353
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