Hemochromatosis gromacs energy table pictures

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Revision as of 17:50, 25 June 2012 by Joerdensv (talk | contribs) (Tables)
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Tables

<figtable id="charmm27-table">

Mutation Step Bond Potential
charmm27foldX_A162S 416.000000 911.913208 -38642.117188
charmm27foldX_A162S_WT 414.000000 912.089478 -38686.621094
charmm27foldX_C282S 434.000000 913.239929 -38589.964844
charmm27foldX_C282S_WT 500.000000 924.356506 -38874.335938
charmm27foldX_E277K 430.000000 911.529053 -38557.769531
charmm27foldX_E277K_WT 459.000000 915.498230 -38748.359375
charmm27foldX_G93R 399.000000 918.111633 -39702.589844
charmm27foldX_G93R_WT 384.000000 909.011108 -38604.292969
charmm27foldX_L183P 414.000000 915.552612 -38457.714844
charmm27foldX_L183P_WT 392.000000 911.028076 -38654.937500
charmm27foldX_M35T 409.000000 914.066162 -38787.164062
charmm27foldX_M35T_WT 483.000000 918.399475 -38843.636719
charmm27foldX_Q127H 500.000000 922.999756 -38733.972656
charmm27foldX_Q127H_WT 498.000000 923.042114 -38891.468750
charmm27foldX_R224W 499.000000 918.184448 -37634.843750
charmm27foldX_R224W_WT 423.000000 912.450745 -38684.457031
charmm27foldX_T217I 500.000000 923.034302 -38771.113281
charmm27foldX_T217I_WT 500.000000 920.963379 -38851.589844
charmm27foldX_V53M 500.000000 919.746765 -38904.714844
charmm27foldX_V53M_WT 427.000000 912.595825 -38751.250000
charmm27scwrl_A162S 493.000000 928.129150 -38806.101562
charmm27scwrl_C282S 500.000000 926.424072 -38715.519531
charmm27scwrl_E277K 500.000000 922.746704 -38652.375000
charmm27scwrl_G93R 500.000000 937.159790 -39957.160156
charmm27scwrl_L183P 500.000000 933.260010 -38573.492188
charmm27scwrl_M35T 432.000000 919.643250 -38756.308594
charmm27scwrl_Q127H 488.000000 926.190369 -38716.339844
charmm27scwrl_R224W 500.000000 924.948364 -37588.648438
charmm27scwrl_T217I 500.000000 929.191162 -38751.257812
charmm27scwrl_V53M 500.000000 925.480591 -38804.257812
charmm27scwrl_WT 500.000000 926.869995 -38812.652344
Table TODO: TODO

</figtable>




<figtable id="amber03-table">

Mutation Step Bond Angle Potential
amber03foldX_A162S 500.000000 491.628113 2726.369141 -35122.839844
amber99sb-ildnfoldX_A162S 411.000000 548.428772 2829.568848 -42459.734375
amber03foldX_A162S_WT 465.000000 488.298706 2727.959473 -35008.968750
amber99sb-ildnfoldX_A162S_WT 411.000000 549.143311 2825.947021 -42442.929688
amber03foldX_C282S 461.000000 487.568878 2732.329102 -34902.957031
amber99sb-ildnfoldX_C282S 411.000000 549.390625 2828.051758 -42387.605469
amber03foldX_C282S_WT 436.000000 485.605164 2733.264404 -34935.320312
amber99sb-ildnfoldX_C282S_WT 430.000000 549.207642 2828.042480 -42433.660156
amber03foldX_E277K 411.000000 483.082153 2733.909424 -34586.335938
amber99sb-ildnfoldX_E277K 450.000000 549.789795 2826.137451 -42290.179688
amber03foldX_E277K_WT 500.000000 491.365387 2725.939453 -35042.156250
amber99sb-ildnfoldX_E277K_WT 410.000000 549.350708 2826.068848 -42442.281250
amber03foldX_G93R 412.000000 488.639648 2738.803955 -35611.089844
amber99sb-ildnfoldX_G93R 403.000000 557.051208 2834.081543 -43169.542969
amber03foldX_G93R_WT 437.000000 485.531738 2731.121826 -35081.218750
amber99sb-ildnfoldX_G93R_WT 408.000000 549.187622 2825.667236 -42462.242188
amber03foldX_L183P 377.000000 483.799500 2766.614014 -34694.523438
amber99sb-ildnfoldX_L183P 431.000000 551.478882 2860.221436 -42201.164062
amber03foldX_L183P_WT 463.000000 488.210205 2726.013428 -35005.070312
amber99sb-ildnfoldX_L183P_WT 405.000000 547.895203 2824.677490 -42419.527344
amber03foldX_M35T 499.000000 490.753815 2731.586182 -35207.015625
amber99sb-ildnfoldX_M35T 398.000000 548.453735 2834.165283 -42549.324219
amber03foldX_M35T_WT 500.000000 490.350128 2731.472900 -35056.296875
amber99sb-ildnfoldX_M35T_WT 431.000000 551.399170 2830.634766 -42482.703125
amber03foldX_Q127H 443.000000 487.118530 2811.132080 -34757.441406
amber99sb-ildnfoldX_Q127H 437.000000 551.995483 2902.304688 -42259.121094
amber03foldX_Q127H_WT 279.000000 468.112152 2735.121094 -34561.304688
amber99sb-ildnfoldX_Q127H_WT 410.000000 548.062073 2830.985596 -42440.109375
amber03foldX_R224W 484.000000 486.756226 2730.202148 -34353.531250
amber99sb-ildnfoldX_R224W 413.000000 539.858215 2828.609131 -41523.914062
amber03foldX_R224W_WT 449.000000 489.200500 2730.227539 -34956.691406
amber99sb-ildnfoldX_R224W_WT 359.000000 544.189209 2828.104736 -42281.617188
amber03foldX_T217I 454.000000 490.702209 2736.986572 -34824.484375
amber99sb-ildnfoldX_T217I 469.000000 554.951294 2827.989258 -42393.929688
amber03foldX_T217I_WT 469.000000 487.084595 2728.806641 -34984.101562
amber99sb-ildnfoldX_T217I_WT 278.000000 535.512634 2823.761475 -42123.968750
amber03foldX_V53M 468.000000 484.353394 2717.921631 -35002.503906
amber99sb-ildnfoldX_V53M 321.000000 537.884521 2815.856934 -42196.277344
amber03foldX_V53M_WT 499.000000 489.776550 2712.700928 -35080.843750
amber99sb-ildnfoldX_V53M_WT 378.000000 544.699585 2814.333008 -42392.343750
amber03scwrl_A162S 446.000000 489.782104 2719.646729 -34788.820312
amber99sb-ildnscwrl_A162S 477.000000 553.757019 2813.325928 -42418.507812
amber03scwrl_C282S 472.000000 488.935638 2708.616699 -34695.152344
amber99sb-ildnscwrl_C282S 407.000000 548.147949 2805.448975 -42232.640625
amber03scwrl_E277K 479.000000 487.748413 2715.674072 -34448.855469
amber99sb-ildnscwrl_E277K 402.000000 544.935852 2814.166016 -42060.632812
amber03scwrl_G93R 453.000000 493.024719 2714.307373 -35355.242188
amber99sb-ildnscwrl_G93R 468.000000 562.177612 2810.380371 -43178.710938
amber03scwrl_L183P 325.000000 480.905640 2740.796875 -34343.757812
amber99sb-ildnscwrl_L183P 344.000000 544.525330 2831.428955 -41881.765625
amber03scwrl_M35T 397.000000 483.174225 2714.149170 -34749.484375
amber99sb-ildnscwrl_M35T 458.000000 551.421387 2804.754639 -42476.714844
amber03scwrl_Q127H 384.000000 483.427490 2787.176758 -34257.574219
amber99sb-ildnscwrl_Q127H 423.000000 550.531982 2878.031738 -42057.433594
amber03scwrl_R224W 500.000000 489.265625 2709.783447 -34167.886719
amber99sb-ildnscwrl_R224W 499.000000 550.281860 2805.838867 -41575.382812
amber03scwrl_T217I 469.000000 493.073303 2714.950439 -34627.269531
amber99sb-ildnscwrl_T217I 444.000000 551.933533 2810.318848 -42198.093750
amber03scwrl_V53M 374.000000 482.391785 2717.136719 -34590.843750
amber99sb-ildnscwrl_V53M 386.000000 548.273010 2810.422363 -42180.039062
amber03scwrl_WT 400.000000 485.167786 2712.698242 -34643.476562
amber99sb-ildnscwrl_WT 424.000000 548.481323 2805.496094 -42275.007812
Table TODO:TODO.

</figtable>

Pictures

<figtable id="V53M_pymol">

M35T
Modelenergies based on the foldX M35T mutation.The used forcefield was Amber03.
Modelenergies based on the scwrl M35T mutation.The used forcefield was Amber03.
V53M
Modelenergies based on the foldX V53M mutation.The used forcefield was Amber03.
Modelenergies based on the scwrlV53M mutation.The used forcefield was Amber03.
Q93R
Modelenergies based on the foldX Q93R mutation.The used forcefield was Amber03.
Modelenergies based on the scwrl Q93R mutation.The used forcefield was Amber03.
Q127H
Modelenergies based on the foldX Q127H mutation.The used forcefield was Amber03.
Modelenergies based on the scwrl Q127H mutation.The used forcefield was Amber03.
A162S
Modelenergies based on the foldX A162S mutation.The used forcefield was Amber03.
Modelenergies based on the scwrl A162S mutation.The used forcefield was Amber03.
Table TODO: Plots of the energy values (bond, angle and potential) of the model .

<figtable id="V53M_pymol">

L183P
Modelenergies based on the foldX L183P mutation.The used forcefield was Amber03.
Modelenergies based on the scwrl L183P mutation.The used forcefield was Amber03.
T217I
Modelenergies based on the foldX T217I mutation.The used forcefield was Amber03.
Modelenergies based on the scwrl T217I mutation.The used forcefield was Amber03.
R224W
Modelenergies based on the foldX R224W mutation.The used forcefield was Amber03.
Modelenergies based on the scwrl R224W mutation.The used forcefield was Amber03.
E277K
Modelenergies based on the foldX E277K mutation.The used forcefield was Amber03.
Modelenergies based on the scwrl E277K mutation.The used forcefield was Amber03.
C282S
Modelenergies based on the foldX C282S mutation.The used forcefield was Amber03.
Modelenergies based on the scwrl C282S mutation.The used forcefield was Amber03.
Table TODO: Plots of the energy values (bond, angle and potential) of the model .


<figtable id="V53M_pymol">

Wildtypes (Amber03)
Wildtype modelenergies based on the foldX M35T mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the foldX V53M mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the foldX G93R mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the foldX Q127H mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the foldX A162S mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the foldX L183P mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the foldX T217I mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the foldX R224W mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the foldX E277K mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the foldX C282S mutation.The used forcefield was Amber03.
Wildtype modelenergies based on the scwrl method. The used forcefield was Amber03.
Wildtypes (Amber99sb-ildn)
Wildtype modelenergies based on the foldX M35T mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the foldX V53M mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the foldX G93R mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the foldX Q127H mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the foldX A162S mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the foldX L183P mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the foldX T217I mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the foldX R224W mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the foldX E277K mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the foldX C282S mutation.The used forcefield was Amber99sb-ildn.
Wildtype modelenergies based on the scwrl method.The used forcefield was Amber99sb-ildn.
Wildtypes (Charmm27)
Wildtype modelenergies based on the foldX M35T mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the foldX V53M mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the foldX G93R mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the foldX Q127H mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the foldX A162S mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the foldX L183P mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the foldX T217I mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the foldX R224W mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the foldX E277K mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the foldX C282S mutation.The used forcefield was Charmm27.
Wildtype modelenergies based on the scwrl method. The used forcefield was Charmm27.
Table TODO: Plots of the energy values (bond, angle and potential) of the model .