# Difference between revisions of "Normal mode analysis HEXA"

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=== Comparison to NOMAD-Ref === |
=== Comparison to NOMAD-Ref === |
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+ | Next, we want to compare the result of All-atom NMA with an elastic network calculation (NOMAD-Ref). |
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+ | {| border="1" style="text-align:center; border-spacing:0;" |
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+ | |model 7 |
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+ | |model 9 |
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+ | |[[Image:mode7.png|thumb|150px|normalized squared atomic displacments of model 7]] |
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+ | |[[Image:mode8.png|thumb|150px|normalized squared atomic displacments of model 8]] |
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+ | |[[Image:mode9.png|thumb|150px|normalized squared atomic displacments of model 9]] |
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+ | |} |

## Revision as of 14:18, 14 July 2011

## Contents

## Webnma

#### General information

#### Results

We analysed the five models with the lowest energy values. Webnma calculates fourteen different models with following energy values:

Mode Index | Deformation Energy |

7 | 1041.88 |

8 | 1318.21 |

9 | 1738.30 |

10 | 2841.31 |

11 | 3135.09 |

12 | 4100.18 |

13 | 3911.06 |

14 | 5337.50 |

15 | 5741.69 |

16 | 6513.85 |

17 | 6081.05 |

18 | 6882.96 |

19 | 7514.14 |

20 | 7943.67 |

We took the first five models (7, 8, 9, 10, 11).

Here you can see the normalized squared atomic displacments of our models:

model 7 | model 8 | model 9 | model 10 | model 11 |

Here you can see the motion of our analyses.

model 7 | model 8 | model 9 | model 10 | model 11 |

#### Discussion

## El Nemo

#### General information

#### Results

Here you can see the CA distance fluctuations for the different modes:

This matrix displays the maximum distance fluctuations between all pairs of CA atoms and between the two extreme conformations that were computed for this mode (DQMIN/DQMAX). Distance increases are plotted in blue and decreases in red for the strongest 10% of the residue pair distance changes. Every pixel corresponds to a single residue. Grey lines are drawn every 10 residues, yellow lines every 100 residues (counting from the upper left corner).

model 7 | model 8 | model 9 | model 10 | model 11 |

El Nemo provides three different animated gif to the user, which show the motions of the protein. Furthermore, we created another animated gif. Therefore, in this case we have four different anmiated gifs. We listed all gifs for one model in on line.

**Model 7:**

picture from use | picture 1 from ElNemo | picture 2 from ElNemo | picture 3 from ElNemo |

**Model 8:**

picture from use | picture 1 from ElNemo | picture 2 from ElNemo | picture 3 from ElNemo |

**Model 9:**

picture from use | picture 1 from ElNemo | picture 2 from ElNemo | picture 3 from ElNemo |

**Model 10:**

picture from use | picture 1 from ElNemo | picture 2 from ElNemo | picture 3 from ElNemo |

**Model 11:**

picture from use | picture 1 from ElNemo | picture 2 from ElNemo | picture 3 from ElNemo |

#### Discussion

## Anisotropic Network Model web server

#### General information

#### Results

Here you can see the B-factor distribution of the real occuring B-factors (black) and the calulated B-factors (blue).

model 1 | model 2 | model 3 | model 4 | model 5 |

In the next table, the motion of the protein of the different models is shown:

model 1 | model 2 | model 3 | model 4 | model 5 |

#### Discussion

## NOMAD-Ref

### General information

### Results

model 1 | model 2 | model 3 | model 4 | model 5 |

model 1 | model 2 | model 3 | model 4 | model 5 |

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

### General information

### Results

#### 600K

Here you can see the motion of 1BPT at temprature 600K.

model 7 | model 8 | model 9 |

#### 2000K

Here you can see the motion of 1BPT at temprature 2000K.

model 7 | model 8 | model 9 |

### Comparison to NOMAD-Ref

Next, we want to compare the result of All-atom NMA with an elastic network calculation (NOMAD-Ref).

model 7 | model 8 | model 9 |