Difference between revisions of "Normal Mode Analysis BCKDHA"

From Bioinformatikpedia
(NOMAD-Ref)
(All-atom NMA using Gromacs on the NOMAD-Ref server)
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In order to do the all-atom NMA we needed to prepare our PDB file. The PDB file for 1BPT protein contains 1629 atoms in total, all lines not beginning with "ATOM" were removed from the PDB file.
 
In order to do the all-atom NMA we needed to prepare our PDB file. The PDB file for 1BPT protein contains 1629 atoms in total, all lines not beginning with "ATOM" were removed from the PDB file.
   
<!-- A second small protein was chosen for the all atom analysis. In order to find an appropriate small protein, we searched for "all atom nma" and found a paper <ref>Hetunandan Kamisetty, Eric P. Xing and Christopher J. Langmead: Free Energy Estimates of All-atom Protein
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A second small protein was chosen for the all atom analysis. In order to find an appropriate small protein, we searched for "all atom nma" and found a paper <ref>Hetunandan Kamisetty, Eric P. Xing and Christopher J. Langmead: Free Energy Estimates of All-atom Protein
 
Structures Using Generalized Belief Propagation[[http://www.cs.cmu.edu/~epxing/papers/recomb-hetu.pdf]]</ref>.
 
Structures Using Generalized Belief Propagation[[http://www.cs.cmu.edu/~epxing/papers/recomb-hetu.pdf]]</ref>.
 
They used the structure of a hen egg-white lysozyme for an all atom NMA. So we did all the calculations for the corresponding PDB entry 2lyz, too.
 
They used the structure of a hen egg-white lysozyme for an all atom NMA. So we did all the calculations for the corresponding PDB entry 2lyz, too.
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-->
 
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{| border="1" style="text-align:center; border-spacing:0;"
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|mode 1
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|mode 2
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|mode 3
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|mode 4
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|mode 5
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|-
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|[[Image:2LYZ_200K_mode7.gif|thumb|150px|All atom normal mode 1 at 200K]]
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|[[Image:2LYZ_200K_mode8.gif|thumb|150px|All atom normal mode 2 at 200K]]
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|[[Image:2LYZ_200K_mode8.gif|thumb|150px|All atom normal mode 3 at 200K]]
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|}
   
 
== Advantages and Disadvantages from NMA and MD ==
 
== Advantages and Disadvantages from NMA and MD ==

Revision as of 22:03, 18 July 2011

WEBnm@

ElNemo

Anisotropic Network Model web server

oGNM – Gaussian network model

NOMAD-Ref

The NOMAD <ref>[[1]]</ref> server provides a lot of information and options. The interface is quite user friendly as all available parameter choices are explained in detail and there is also the runtime listed for an example NMA, which can be used to estimate the runtime for our own jobs.

The following parameters can be set:

Number of modes to calculate
As specified in the task description we wanted to obtain 10 modes. NOMAD does six zero modes which are just translation and rotation. Therefore we set the number of modes to calculate to 16.
Distance weight parameter
This parameter is used to introduce a smoother cutoff value that in the original Tirion model. All distances are weightend by exp(-(d_ij/d)^2), where d is the distance weight parameter. As proposed by NOMAD a distance weight parameter of 3Å is well suited for CA-only models. As we are doing no all-atom calculation, the distance weight parameter was set to 3.0Å.
Cutoff to use for mode calculation
The cutoff describes which pairs of atomes are linked by a spring of universal length according to the Tirion model (Elastic Network Model). The cutoff was set to 15Å.
Average Rmsd in output trajectories
For the average RMSD the default value (3.0) was used.
Method to use
    • Automatic
    • Full matrix solver
    • Sparse matrix solver
Here we used the default option, the automatic mode.

The output contains one PDB file and one plot per mode. The plot contains the rmsd per residue, which can be interpreted as the amplitude of movement and which is controlled by the average rmsd of trajectory (input parameter).

What information do the different servers provide? Which regions of your protein are most flexible, most stable? When you visualize the modes (provided by server or using for example PyMol or VMD), try to describe what movements you observe? Hinge-movement, “breathing”…

mode 1 mode 2 mode 3 mode 4 mode 5
NOMAD normal mode 1
NOMAD normal mode 2
NOMAD normal mode 3
NOMAD normal 4
NOMAD normal 5
Amplitude of movement as rmsd per residue for mode 1
Amplitude of movement as rmsd per residue for mode 2
Amplitude of movement as rmsd per residue for mode 3
Amplitude of movement as rmsd per residue for mode 4
Amplitude of movement as rmsd per residue for mode 5
Elastic network for mode 1
Elastic network for mode 2
Elastic network for mode 3
Elastic network for mode 4
Elastic network for mode 5

All-atom NMA using Gromacs on the NOMAD-Ref server

In order to do the all-atom NMA we needed to prepare our PDB file. The PDB file for 1BPT protein contains 1629 atoms in total, all lines not beginning with "ATOM" were removed from the PDB file.

A second small protein was chosen for the all atom analysis. In order to find an appropriate small protein, we searched for "all atom nma" and found a paper <ref>Hetunandan Kamisetty, Eric P. Xing and Christopher J. Langmead: Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation[[2]]</ref>. They used the structure of a hen egg-white lysozyme for an all atom NMA. So we did all the calculations for the corresponding PDB entry 2lyz, too.


mode 1 mode 2 mode 3 mode 4 mode 5
All atom normal mode 1 at 200K
All atom normal mode 2 at 200K
All atom normal mode 3 at 200K

Advantages and Disadvantages from NMA and MD

References

<references />

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