Team:EPF-Lausanne/Analysis methods

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<a href="https://2009.igem.org/Team:EPF-Lausanne/Modeling_overview" onMouseOver="document.MyImage7.src='https://static.igem.org/mediawiki/2009/8/83/Modeling_overview.jpg';" onMouseOut="document.MyImage7.src='https://static.igem.org/mediawiki/2009/6/6d/Modeling_overview_grey.jpg';">
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Analysis_methods" onMouseOver="document.MyImage4.src='https://static.igem.org/mediawiki/2009/thumb/6/6e/An_meth.png/150px-An_meth.png';" onMouseOut="document.MyImage4.src='https://static.igem.org/mediawiki/2009/thumb/6/6e/An_meth.png/150px-An_meth.png';">
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Results" onMouseOver="document.MyImage6.src='https://static.igem.org/mediawiki/2009/thumb/2/2f/Results.jpg/150px-Results.jpg';" onMouseOut="document.MyImage6.src='https://static.igem.org/mediawiki/2009/thumb/4/43/Results_nb.jpg/150px-Results_nb.jpg';">
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Information_&_references" onMouseOver="document.MyImage5.src='https://static.igem.org/mediawiki/2009/thumb/a/a2/Ref.jpg/150px-Ref.jpg';" onMouseOut="document.MyImage5.src='https://static.igem.org/mediawiki/2009/thumb/2/25/Ref_nb.jpg/150px-Ref_nb.jpg';">
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----
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<font size="6" color="#007CBC"><i>Analysis Methods</i></font>  
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<font size="12" color="#007CBC">Analysis Methods</font>  
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----
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=Softwares used=
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===VMD===
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VMD is a molecular visualization program for displaying, animating, and analyzing biomolecular systems using 3-D graphics and built-in scripting. It provides a wide range of molecular representations, and includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. You can have more information on their [http://www.ks.uiuc.edu/Research/vmd/ webpage].
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===NAMD===
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NAMD is a molecular dynamics code designed for simulation of large biomolecular systems. It is based on Charm++ parallel programming model, and uses VMD for simulation setup and trajectory analysis.
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See their website [http://www.ks.uiuc.edu/Research/namd/ here].
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<br><br>
=Information needed=
=Information needed=
===Generating input files===
===Generating input files===
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In this section, we explain all the steps to create needed files for namd, except the .conf file.
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In this section, we explain all the steps to create needed files for NAMD, except the .conf file, which is just [https://2009.igem.org/Team:EPF-Lausanne/Analysis_methods#Namd_.conf_parameters below].
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We need a compatible .pdb in addition to parameter and topology files to go through. Steps to generate all the input files are explained in detail on this page [[Team:EPF-Lausanne/Modeling/Simulation|How to generate input files]]. This is a kind of summary of the tuto.
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We need a compatible .pdb in addition to parameter and topology files to go through. Steps to generate all the input files are explained in detail on this page:
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[[Team:EPF-Lausanne/Modeling/Simulation|How to generate input files]]. This is a kind of summary of the tutorial.
===Launch a simulation===
===Launch a simulation===
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Here we will analyze the temperature distribution over the simulation. The temperature might increase linearly during the heating step and then it might remain stable.
Here we will analyze the temperature distribution over the simulation. The temperature might increase linearly during the heating step and then it might remain stable.
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We obtained the expected [https://2009.igem.org/Team:EPF-Lausanne/Results results].
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We obtained the expected [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Validation#Temperature results].
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Here we will analyze the behavior of the protein density over the simulation. Normally during the equilibration step density might remain more or less stable. Particularly during the NVT equilibration the density might remain constant.  
Here we will analyze the behavior of the protein density over the simulation. Normally during the equilibration step density might remain more or less stable. Particularly during the NVT equilibration the density might remain constant.  
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We obtained the expected [https://2009.igem.org/Team:EPF-Lausanne/Results results].
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We obtained the expected [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Validation#Density results].
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<script type="text/javascript" language="JavaScript"><!--
<script type="text/javascript" language="JavaScript"><!--
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In order to obtain the data for the volume from the log file we will again use the script <i>namdstats.tcl</i>, which was already sourced. Type in a terminal window:
In order to obtain the data for the volume from the log file we will again use the script <i>namdstats.tcl</i>, which was already sourced. Type in a terminal window:
<br><span style="font-family: Courier;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; data_time VOLUME namd_log </span>
<br><span style="font-family: Courier;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; data_time VOLUME namd_log </span>
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<br>It will store each timestep and its corresponding temperature in the file TEMP.dat.
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<br>It will store each timestep and its corresponding volume in the file VOLUME.dat.
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Here we will analyze the pressure behavior along the minimization and the equilibration. This quantity might stabilize after the heating and remain more or less stable during the equilibration. Particularly during the NPT steps the pressure might be strictly constant.
Here we will analyze the pressure behavior along the minimization and the equilibration. This quantity might stabilize after the heating and remain more or less stable during the equilibration. Particularly during the NPT steps the pressure might be strictly constant.
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We obtained the expected [https://2009.igem.org/Team:EPF-Lausanne/Results results].
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We obtained the expected [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Validation#Pressure results].
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<script type="text/javascript" language="JavaScript"><!--
<script type="text/javascript" language="JavaScript"><!--
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After that we will try after that to select the amino acids to mutate in order to stabilize the light activated state of our LOV domain.
After that we will try after that to select the amino acids to mutate in order to stabilize the light activated state of our LOV domain.
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Click [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Validation#RMSD here] to see the results.
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<script type="text/javascript" language="JavaScript"><!--
<script type="text/javascript" language="JavaScript"><!--
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Here we will analyze the RMSD of each atom to check whether the protein remains more or less stable during the equilibration.
Here we will analyze the RMSD of each atom to check whether the protein remains more or less stable during the equilibration.
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We obtained the expected [https://2009.igem.org/Team:EPF-Lausanne/Results results].
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Click [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/EDS#RMSD here] to see the results for the dark state simulation.
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Click [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here] to see the results for the light state simulation.
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Here we will analyze the evolution of these interactions over the equilibration in order to check how these interactions change over the equilibration.
Here we will analyze the evolution of these interactions over the equilibration in order to check how these interactions change over the equilibration.
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Click [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Validation#Salt_bridges here] to see the results.
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<script type="text/javascript" language="JavaScript"><!--
<script type="text/javascript" language="JavaScript"><!--
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This is quite similar to the RMSD analysis. Here we will analyze how the RMSF vary for each residues.  
This is quite similar to the RMSD analysis. Here we will analyze how the RMSF vary for each residues.  
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Click [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here] to see the results for the dark state simulation.
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Click [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSF here] to see the results for the light state simulation.
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<script type="text/javascript" language="JavaScript"><!--
<script type="text/javascript" language="JavaScript"><!--
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This part is made to measure the angle between two chains. The procedure is described below.
This part is made to measure the angle between two chains. The procedure is described below.
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Click [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#Angle_between_beta_sheet_and_alpha_helix here] to see the results for the dark state simulation.
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Click [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#Angle_between_beta_sheet_and_alpha_helix here] to see the results for the light state simulation.
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== H bonds and distance measurments ==
== H bonds and distance measurments ==
This part aim at finding characteristic distances, in particular for H-bonds.
This part aim at finding characteristic distances, in particular for H-bonds.
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Click [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#Some_useful_distances here] to see the results for the dark state simulation.
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Dihedral angles measure angle between four atoms.
Dihedral angles measure angle between four atoms.
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Click [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#CYS450_-_FMN here] to see the results for the dark state simulation.
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Click [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#CYS450_-_FMN here] to see the results for the light state simulation.
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== PCA Analysis ==
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PCA is a useful technique used for compression and data classification.
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<a href="javascript:ReverseDisplay('hs14')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to expand</a>
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The aim is to reduce the dimensionality (number of dimensions) of a data ensemble (sample), by finding a new set of variables with a smaller size than the original set of variables. However, this new set must contain the main part of the information: most of the information is kept in a smaller number of variables.
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Information means variation in the sample, et given by the correlation between the original variables. The new variables are called principal components (PC), and are not correlated. They are given by splitting the total information contained in each one.
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Latest revision as of 19:21, 21 October 2009






                                               




Analysis Methods



Softwares used

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing biomolecular systems using 3-D graphics and built-in scripting. It provides a wide range of molecular representations, and includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. You can have more information on their webpage.

NAMD

NAMD is a molecular dynamics code designed for simulation of large biomolecular systems. It is based on Charm++ parallel programming model, and uses VMD for simulation setup and trajectory analysis. See their website here.



Information needed

Generating input files

In this section, we explain all the steps to create needed files for NAMD, except the .conf file, which is just below. We need a compatible .pdb in addition to parameter and topology files to go through. Steps to generate all the input files are explained in detail on this page: How to generate input files. This is a kind of summary of the tutorial.

Launch a simulation

We start from .pdb, .psf, .rtf generated in the previous sections and we explain how to launch NAMD on both clusters we have access to. Complete process is on a separate page How to launch a simulation.

Namd .conf parameters

Namd can run different kind of simulations, from minimization to MD simulations. Here are the .conf file we used. NamdConf

Scripts used

We stored all our scripts, which were highly modified compared to the original ones, in order to fit our needs. You can find them on this page.



Step by step analysis

The following section is a kind of tutorial, which describes step by step how to obtain our different results.

This analysis will check whether the minimization, the heating and the equilibration took place correctly and whether the protein did not explode.

Maxwell-Boltzmann Energy Distribution

Here we will confirm that the kinetic energy distribution of the atoms in a system corresponds to the Maxwell distribution for a given temperature.

         Click here to expand


Energies

Here we will calculate the average of various energies such as kinetic energy and different internal ones so called bonded energies (bonds, angles and dihedrals). Moreover, we will calculate non-bonded energy (electrostatic, van der Waals)) over the course of the equilibration.

         Click here to expand


Temperature distribution

Here we will analyze the temperature distribution over the simulation. The temperature might increase linearly during the heating step and then it might remain stable.

We obtained the expected results.

         Click here to expand


Density

Here we will analyze the behavior of the protein density over the simulation. Normally during the equilibration step density might remain more or less stable. Particularly during the NVT equilibration the density might remain constant.

We obtained the expected results.

         Click here to expand


Pressure as a function of simulation time

Here we will analyze the pressure behavior along the minimization and the equilibration. This quantity might stabilize after the heating and remain more or less stable during the equilibration. Particularly during the NPT steps the pressure might be strictly constant.

We obtained the expected results.

         Click here to expand


RMSD for individual residues

Here we will calculate the RMSD for each residue to determine which residue move the most. This analysis will help us to see which residue is more or less stable. After that we will try after that to select the amino acids to mutate in order to stabilize the light activated state of our LOV domain.

Click here to see the results.

         Click here to expand


RMSD of selected atoms compared to initial position along time

Here we will analyze the RMSD of each atom to check whether the protein remains more or less stable during the equilibration.

Click here to see the results for the dark state simulation.

Click here to see the results for the light state simulation.

         Click here to expand


Salt bridges

Salt bridges are non-bonded interactions between charged residues.

Here we will analyze the evolution of these interactions over the equilibration in order to check how these interactions change over the equilibration.

Click here to see the results.

         Click here to expand


RMSF

This is quite similar to the RMSD analysis. Here we will analyze how the RMSF vary for each residues.

Click here to see the results for the dark state simulation.

Click here to see the results for the light state simulation.

         Click here to expand



Angles

This part is made to measure the angle between two chains. The procedure is described below.

Click here to see the results for the dark state simulation.

Click here to see the results for the light state simulation.

         Click here to expand



H bonds and distance measurments

This part aim at finding characteristic distances, in particular for H-bonds.

Click here to see the results for the dark state simulation.

         Click here to expand



Dihedral angles

Dihedral angles measure angle between four atoms.

Click here to see the results for the dark state simulation.

Click here to see the results for the light state simulation.

         Click here to expand



PCA Analysis

PCA is a useful technique used for compression and data classification.

         Click here to expand



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