Difference between revisions of "ASPA Structure Based Mutation Analysis"
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===Gromacs=== |
===Gromacs=== |
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+ | |||
+ | 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]] |
[[File:ASPA Timegraph.png]] |
Revision as of 23:45, 31 August 2011
Contents
FoldX
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
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 -nosol and -noh to extract just the protein. Other options available include -seq, which extracts the protein sequence and return it as a string and -cleansol, 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 -seq and edit it to be lowercase with just the mutated position in uppercase.
We measured the run time for different values for nsteps and plotted the results in a graph, with nsteps on the x axis and the time in seconds on the y axis.
Pictures
Wildtype | Mutation | |
RS104894553 | ![]() | ![]() |
CM940124 | ![]() | ![]() |
CM063847 | ![]() | ![]() |
RS80099330 | ![]() | ![]() |
CM990193 | ![]() | ![]() |
RS104894548 | ![]() | ![]() |
CM990195 | ![]() | ![]() |
CM055097 | ![]() | ![]() |
RS104894551 | ![]() | ![]() |
CM994594 | ![]() | ![]() |
cm055097
Mut 2O53 cm055097 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
cm055097
Mut 2O53 cm055097 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
cm055097
Mut 2O53 cm063847 onlyprot A gromacs angle.png
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |
cm063847
Mut 2O53 cm063847 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
cm063847
Mut 2O53 cm063847 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
cm063847
Mut 2O53 cm940124 onlyprot A gromacs angle.png
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |
cm940124
Mut 2O53 cm940124 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
cm940124
Mut 2O53 cm940124 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
cm940124
Mut 2O53 cm990193 onlyprot A gromacs angle.png
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |
cm990193
Mut 2O53 cm990193 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
cm990193
Mut 2O53 cm990193 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
cm990193
Mut 2O53 cm990195 onlyprot A gromacs angle.png
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |
cm990195
Mut 2O53 cm990195 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
cm990195
Mut 2O53 cm990195 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
cm990195
Mut 2O53 cm994594 onlyprot A gromacs angle.png
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |
cm994594
Mut 2O53 cm994594 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
cm994594
Mut 2O53 cm994594 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
cm994594
Mut 2O53 rs104894548 onlyprot A gromacs angle.png
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |
rs104894548
Mut 2O53 rs104894548 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
rs104894548
Mut 2O53 rs104894548 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
rs104894548
Mut 2O53 rs104894551 onlyprot A gromacs angle.png
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |
rs104894551
Mut 2O53 rs104894551 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
rs104894551
Mut 2O53 rs104894551 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
rs104894551
Mut 2O53 rs104894553 onlyprot A gromacs angle.png
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |
rs104894553
Mut 2O53 rs104894553 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
rs104894553
Mut 2O53 rs104894553 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
rs104894553
Mut 2O53 rs80099330 onlyprot A gromacs angle.png
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |
rs80099330
Mut 2O53 rs80099330 onlyprot A gromacs bond.png
Average | Err.Est. | RMSD | Tot-Drift | ||
angle | avg | errest | rmsd | totdrift | ![]() |
rs80099330
Mut 2O53 rs80099330 onlyprot A gromacs potential.png
Average | Err.Est. | RMSD | Tot-Drift | ||
bond | avg | errest | rmsd | totdrift | ![]() |
rs80099330
Average | Err.Est. | RMSD | Tot-Drift | ||
potential | avg | errest | rmsd | totdrift | ![]() |