Normal mode analysis GLA

From Bioinformatikpedia
Revision as of 23:42, 29 August 2011 by Drexler (talk | contribs) (WEBnm@)

by Benjamin Drexler and Fabian Grandke

Introduction

Methods

WEBnm@

The normal mode analysis webserver WEBnm@ was published by Siv Midtun Hollup, Gisle Salensminde and Nathalie Reuter in 2005<ref name=webnma>Siv Midtun Hollup, Gisle Salensminde and Nathalie Reuter. "WEBnm@: a web application for normal mode analyses of proteins". BMC Bioinformatics 2005, 6:52. PubMed</ref>. It allows the calculation of the normal modes and offers serveral types of analyses, i.e. deformation energy, animation of the vibration, atomic squared displacements and vector field analysis.

Usage

  • Webserver: http://apps.cbu.uib.no/webnma/home
  • Input
    • PDB structure (ID or file)
    • Specification of chains
  • Output
    • Animation of vibration
    • Deformation energy
    • Squared atomic displacements

ElNemo

Anisotropic Network Model

oGNM

NOMAD-Ref

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

Results & Discussion

WEBnm@

ElNemo

Anisotropic Network Model

oGNM

NOMAD-Ref

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

References

<references/>