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==FoldX== {| border="1" style="font-size:x-small" |- ! Mutation ! BackHbond ! SideHbond ! Energy_VdW ! Electro ! SolvP ! SolvH ! vdwclash ! torsion ! bb_vdwclash ! Entropy_sidec ! Entropy_mainc ! water bonds ! helix dipole ! loop_entropy ! cis_bond ! disulfide ! kn electrostatic ! partial covalent interactions ! Ionisation ! Entropy Complex ! Total |- | WT | -351.60 | -113.32 | -753.77 | -34.77 | 991.74 | -1003.86 | 94.80 | 42.16 | 375.34 | 372.13 | 941.00 | -1.73 | -1.78 | 0.00 | 9.05 | 0.00 | -0.94 | -26.09 | 2.96 | 0.00 | 165.97 |- | CM055097 | -355.76 | -113.21 | -759.56 | -33.94 | 986.09 | -1010.92 | 170.97 | 80.70 | 377.29 | 374.36 | 942.29 | 0.00 | -1.21 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 3.65 | 0.00 | 291.86 |- | CM063847 | -355.74 | -112.37 | -759.94 | -34.09 | 985.12 | -1012.35 | 178.46 | 80.88 | 377.32 | 374.49 | 942.56 | 0.00 | -1.44 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 3.68 | 0.00 | 297.66 |- | CM940124 | -355.67 | -113.51 | -760.79 | -33.98 | 989.54 | -1012.11 | 185.56 | 80.68 | 377.55 | 375.73 | 942.35 | 0.00 | -1.76 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 3.64 | 0.00 | 308.08 |- | CM990193 | -355.77 | -113.23 | -760.51 | -33.74 | 987.84 | -1011.65 | 194.71 | 80.60 | 377.51 | 374.59 | 944.00 | 0.00 | -1.44 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 3.79 | 0.00 | 317.61 |- | CM990195 | -355.82 | -113.22 | -759.67 | -34.61 | 989.16 | -1009.25 | 179.53 | 80.75 | 377.29 | 374.77 | 942.43 | 0.00 | -1.36 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 3.64 | 0.00 | 304.76 |- | CM994594 | -355.60 | -113.20 | -756.93 | -33.66 | 982.92 | -1007.28 | 169.81 | 80.49 | 376.73 | 373.69 | 941.91 | 0.00 | -1.44 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 3.64 | 0.00 | 292.75 |- | RS104894548 | -355.81 | -113.21 | -760.68 | -33.70 | 989.00 | -1011.59 | 187.60 | 80.73 | 377.34 | 375.06 | 942.60 | 0.00 | -1.39 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 3.64 | 0.00 | 310.63 |- | RS104894551 | -355.68 | -113.48 | -757.12 | -31.38 | 979.51 | -1008.38 | 168.90 | 80.33 | 376.85 | 372.68 | 942.57 | 0.00 | -1.45 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 3.11 | 0.00 | 288.02 |- | RS104894553 | -355.73 | -113.24 | -759.08 | -35.12 | 985.71 | -1010.41 | 173.40 | 80.55 | 377.28 | 374.26 | 942.65 | 0.00 | -1.41 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 4.03 | 0.00 | 294.00 |- | RS80099330 | -355.61 | -113.21 | -758.06 | -33.77 | 984.24 | -1008.91 | 170.10 | 80.58 | 377.03 | 373.24 | 942.10 | 0.00 | -1.44 | 0.00 | 9.03 | 0.00 | -0.63 | 0.00 | 3.64 | 0.00 | 291.29 |- |} ==Minimise== {| border="1" style="font-size:x-small" |- ! Mutation | WT | cm055097 | cm063847 | cm940124 | cm990193 | cm990195 | cm994594 | rs104894548 | rs104894551 | rs104894553 | rs80099330 |- ! Energy | -14776.478983 | -14054.020681 | -12533.719784 | -11003.916326 | -12670.140717 | -11757.261266 | -14164.353463 | -8677.102143 | -14220.689449 | -14035.011150 | -14141.901598 |- |} ===Gromacs=== The script fetchPDB used to download the PDB file first pulls the gzipped version of the PDB file from the PDB website, then unpacks it. We cleaned the PDB file using repairPDB with the options <tt>-nosol</tt> and <tt>-noh</tt> to extract just the protein. Other options available include <tt>-seq</tt>, which extracts the protein sequence and return it as a string and <tt>-cleansol</tt>, which cleans up the solvent for use with Gromacs. We afterwards extracted chain A; since both chains show little in the way of diffences, we decided to use A. Then we generated mutated PDBs using SCWRL; we had to extract the sequence of the protein from the PDB file beforehand using repairPDB with the option <tt>-seq</tt> and edit it to be lowercase with just the mutated position in uppercase. We measured the run time for different values for <tt>nsteps</tt> and plotted the results in a graph, with <tt>nsteps</tt> on the x axis and the time in seconds on the y axis. [[File:ASPA Timegraph.png]] ==Pictures== The following pictures were created using PyMOL to illustrate the effects of the mutations generated by SCWRL: <table> <tr><td> </td><td align=center><b>Wildtype</b></td><td align=center><b>Mutation</b></td></tr> <tr><td><b>RS104894553</b></td><td>[[File:Wt rs104894553.png|500px]]</td><td>[[File:Mut rs104894553.png|500px]]</td></tr> <tr><td><b>CM940124</b></td><td>[[File:Wt cm940124.png|500px]]</td><td>[[File:Mut cm940124.png|500px]]</td></tr> <tr><td><b>CM063847</b></td><td>[[File:Wt cm063847.png|500px]]</td><td>[[File:Mut cm063847.png|500px]]</td></tr> <tr><td><b>RS80099330</b></td><td>[[File:Wt rs80099330.png|500px]]</td><td>[[File:Mut rs80099330.png|500px]]</td></tr> <tr><td><b>CM990193</b></td><td>[[File:Wt cm990193.png|500px]]</td><td>[[File:Mut cm990193.png|500px]]</td></tr> <tr><td><b>RS104894548</b></td><td>[[File:Wt rs104894548.png|500px]]</td><td>[[File:Mut rs104894548.png|500px]]</td></tr> <tr><td><b>CM990195</b></td><td>[[File:Wt cm990195.png|500px]]</td><td>[[File:Mut cm990195.png|500px]]</td></tr> <tr><td><b>CM055097</b></td><td>[[File:Wt cm055097.png|500px]]</td><td>[[File:Mut cm055097.png|500px]]</td></tr> <tr><td><b>RS104894551</b></td><td>[[File:Wt rs104894551.png|500px]]</td><td>[[File:Mut rs104894551.png|500px]]</td></tr> <tr><td><b>CM994594</b></td><td>[[File:Wt cm994594.png|500px]]</td><td>[[File:Mut cm994594.png|500px]]</td></tr> </table> ==Results of the Minimization== The following graphs illustrate the results of the minimization step. <b>cm055097</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm055097 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 cm055097 onlyprot A gromacs bond.png </table><b>cm055097</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm055097 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 cm055097 onlyprot A gromacs potential.png </table><b>cm055097</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm055097 onlyprot A gromacs potential.png|250px]]</td></tr> Mut 2O53 cm063847 onlyprot A gromacs angle.png </table><b>cm063847</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm063847 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 cm063847 onlyprot A gromacs bond.png </table><b>cm063847</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm063847 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 cm063847 onlyprot A gromacs potential.png </table><b>cm063847</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm063847 onlyprot A gromacs potential.png|250px]]</td></tr> Mut 2O53 cm940124 onlyprot A gromacs angle.png </table><b>cm940124</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm940124 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 cm940124 onlyprot A gromacs bond.png </table><b>cm940124</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm940124 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 cm940124 onlyprot A gromacs potential.png </table><b>cm940124</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm940124 onlyprot A gromacs potential.png|250px]]</td></tr> Mut 2O53 cm990193 onlyprot A gromacs angle.png </table><b>cm990193</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm990193 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 cm990193 onlyprot A gromacs bond.png </table><b>cm990193</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm990193 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 cm990193 onlyprot A gromacs potential.png </table><b>cm990193</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm990193 onlyprot A gromacs potential.png|250px]]</td></tr> Mut 2O53 cm990195 onlyprot A gromacs angle.png </table><b>cm990195</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm990195 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 cm990195 onlyprot A gromacs bond.png </table><b>cm990195</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm990195 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 cm990195 onlyprot A gromacs potential.png </table><b>cm990195</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm990195 onlyprot A gromacs potential.png|250px]]</td></tr> Mut 2O53 cm994594 onlyprot A gromacs angle.png </table><b>cm994594</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm994594 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 cm994594 onlyprot A gromacs bond.png </table><b>cm994594</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm994594 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 cm994594 onlyprot A gromacs potential.png </table><b>cm994594</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 cm994594 onlyprot A gromacs potential.png|250px]]</td></tr> Mut 2O53 rs104894548 onlyprot A gromacs angle.png </table><b>rs104894548</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs104894548 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 rs104894548 onlyprot A gromacs bond.png </table><b>rs104894548</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs104894548 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 rs104894548 onlyprot A gromacs potential.png </table><b>rs104894548</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs104894548 onlyprot A gromacs potential.png|250px]]</td></tr> Mut 2O53 rs104894551 onlyprot A gromacs angle.png </table><b>rs104894551</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs104894551 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 rs104894551 onlyprot A gromacs bond.png </table><b>rs104894551</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs104894551 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 rs104894551 onlyprot A gromacs potential.png </table><b>rs104894551</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs104894551 onlyprot A gromacs potential.png|250px]]</td></tr> Mut 2O53 rs104894553 onlyprot A gromacs angle.png </table><b>rs104894553</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs104894553 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 rs104894553 onlyprot A gromacs bond.png </table><b>rs104894553</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs104894553 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 rs104894553 onlyprot A gromacs potential.png </table><b>rs104894553</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs104894553 onlyprot A gromacs potential.png|250px]]</td></tr> Mut 2O53 rs80099330 onlyprot A gromacs angle.png </table><b>rs80099330</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>angle</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs80099330 onlyprot A gromacs angle.png|250px]]</td></tr> Mut 2O53 rs80099330 onlyprot A gromacs bond.png </table><b>rs80099330</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>bond</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs80099330 onlyprot A gromacs bond.png|250px]]</td></tr> Mut 2O53 rs80099330 onlyprot A gromacs potential.png </table><b>rs80099330</b><table><tr><td>Average</td><td>Err.Est.</td><td>RMSD</td><td>Tot-Drift</td><td></td></tr> <tr><td>potential</td><td>avg</td><td>errest</td><td>rmsd</td><td>totdrift</td><td>[[File:Mut 2O53 rs80099330 onlyprot A gromacs potential.png|250px]]</td></tr> </table>

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