Difference between revisions of "Normal Mode Analysis BCKDHA"

From Bioinformatikpedia
(All-atom NMA using Gromacs on the NOMAD-Ref server)
(All-atom NMA using Gromacs on the NOMAD-Ref server)
Line 14: Line 14:
 
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
  +
Structures Using Generalized Belief Propagation[[http://www.cs.cmu.edu/~epxing/papers/recomb-hetu.pdf]]</ref>.
  +
They used the structure of a Lysozyme for an all atom NMA. So we did all the calculations for the corresponding PDB entry 2lyz, too.
  +
-->
  +
  +
  +
== Advantages and Disadvantages from NMA and MD ==
   
 
go back to Task 8: [[Molecular_Dynamics_Simulations_BCKDHA| Molecular Dynamics Simulations]]
 
go back to Task 8: [[Molecular_Dynamics_Simulations_BCKDHA| Molecular Dynamics Simulations]]

Revision as of 13:19, 14 July 2011

WEBnm@

ElNemo

Anisotropic Network Model web server

oGNM – Gaussian network model

NOMAD-Ref

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.


Advantages and Disadvantages from NMA and MD

go back to Task 8: Molecular Dynamics Simulations