Team:KAIST-Korea/Project/Modeling
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Single chain antibody structural alignment
Protocol
There are four steps to compare structure of single chain antibody and FGF binding domain of FGFR. First step is taking variable region sequences of antibodies. Next step is combining these variable region sequences with linker sequence to make single chain antibody sequence. Third step is predicting the structure of single chain antibody with structure prediction program like modeler. Final step is to structural align these structures of antibodies with structure of FGF binding domain of FGFR(PDB ID : 1EVT).
Data source
Single chain antibody synthesis
Structure Prediction
Structure Alignment
Result
Name | Core Residues | Core RMSD | Raw Score | P-value |
---|---|---|---|---|
2VXT | 95 | 2.676 | 84.306 | 0.000222 |
2VXU | 98 | 2.563 | 92.118 | 0.0000823 |
2VXV | 77 | 2.64 | 52.269 | 0.0644 |
2ZKH | 96 | 2.855 | 93.411 | 0.001 |
3AAZ | 84 | 4.197 | 68.078 | 0.0642 |
3D69 | 137 | 12.224 | 98.134 | 0.00541 |
3EO9 | 80 | 2.282 | 84.665 | 0.00295 |
3EOA | 116 | 10.402 | 98.544 | 0.0547 |
3EOB | 68 | 4.685 | 56.357 | 0.3753 |
3EYV | 85 | 4.704 | 66.669 | 0.1653 |
3FMG | 81 | 2.629 | 73.298 | 0.0129 |
3FOG | 90 | 7.243 | 74.031 | 0.0785 |
3G6D | 72 | 4.403 | 69.774 | 0.1281 |
3GBM | 119 | 10.331 | 115.929 | 0.0314 |
3GBN | 77 | 2.788 | 57.204 | 0.0592 |
3GHB | 101 | 12.861 | 81.189 | 0.3984 |
3GHE | 96 | 3.302 | 109.208 | 0.00117 |
3GI8 | 127 | 6.837 | 113.467 | 0.00038 |
3GI9 | 52 | 3.534 | 43.56 | 0.166 |
3GIZ | 89 | 8.217 | 68.702 | 0.3172 |
3GK8 | 91 | 6.84 | 84.048 | 0.00811 |
3GKW | 74 | 3.205 | 47.096 | 0.1215 |
3GNM | 135 | 4.739 | 103.812 | 0.00000297 |
3GO1 | 103 | 8.842 | 77.631 | 0.2587 |
3GRW | 107 | 9.819 | 108.405 | 0.0449 |
3H42 | 69 | 4.389 | 59.165 | 0.3421 |
3HC0 | 67 | 3.065 | 40.982 | 0.1028 |
3HC3 | 67 | 3.173 | 49.109 | 0.0944 |
3HC4 | 36 | 1.998 | 42.538 | 0.206 |
3HI5 | 77 | 3.222 | 58.096 | 0.1832 |
3HI6 | 81 | 3.646 | 63.526 | 0.0394 |
3HMW | 83 | 4.159 | 62.598 | 0.1976 |
3HMX | 70 | 5.215 | 62.814 | 0.2228 |
3HNT | 84 | 2.62 | 74.666 | 0.00118 |
3HNV | 84 | 2.998 | 77.17 | 0.00374 |
3HR5 | 78 | 4.158 | 58.026 | 0.2978 |
3I50 | 65 | 2.206 | 52.252 | 0.1156 |
3I9G | 84 | 5.026 | 64.155 | 0.1506 |
3IU3 | 75 | 3.192 | 56.006 | 0.2552 |
3IXT | 78 | 2.951 | 68.627 | 0.0378 |
3KDM | 87 | 4.273 | 65.722 | 0.1683 |
3KS0 | 81 | 3.039 | 55.562 | 0.0192 |
3KYK | 88 | 4.728 | 68.681 | 0.1016 |
3KYM | 85 | 6.52 | 66.102 | 0.5135 |
3L1O | 93 | 2.545 | 85.909 | 0.0014 |
3L5W | 89 | 4.925 | 72.178 | 0.0637 |
3L5X | 88 | 4.796 | 65.262 | 0.1111 |
3L5Y | 64 | 4.689 | 65.227 | 0.2007 |
3L95 | 73 | 5.105 | 70.312 | 0.0515 |
3LMJ | 76 | 2.699 | 56.627 | 0.0237 |
3LQA | 75 | 8.371 | 58.374 | 0.8315 |
3LS4 | 79 | 2.458 | 72.68 | 0.00694 |
3LS5 | 81 | 2.443 | 73.043 | 0.0014 |
3LZF | 96 | 2.468 | 93.292 | 0.00155 |
3MLR | 71 | 2.574 | 64.979 | 0.0165 |
3MLS | 75 | 2.534 | 57.386 | 0.0202 |
3MLU | 127 | 10.025 | 73.766 | 0.0305 |
3MLV | 75 | 2.454 | 62.321 | 0.0218 |
3MLW | 83 | 8.94 | 59.029 | 0.4846 |
3MLX | 118 | 11.485 | 105.391 | 0.0961 |
3MLY | 84 | 4.704 | 63.962 | 0.1023 |
3MLZ | 82 | 3.995 | 64.563 | 0.123 |
3MUG | 79 | 2.827 | 68.72 | 0.0223 |
3MXV | 125 | 10.857 | 121.911 | 0.01 |
3MXW | 102 | 11.262 | 78.348 | 0.4213 |
16A1 | 86 | 2.139 | 89.893 | 0.00443 |