Normal mode analysis GLA

^{by Benjamin Drexler and Fabian Grandke}

Methods

Brief explanations about the methods and information about the usage are given in the following sections.

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

Karsten Suhre and Yves-Henri Sanejouand published the webserver ElNemo in 2004<ref name=elnemo>Karsten Suhre and Yves-Henri Sanejouand. "ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement". Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W610-4. PubMed</ref>. It is used for the calculation of normal modes and is able to process very large proteins due to a building block approximation. This is, several residues are grouped into a single super residue.

Usage

• Webserver: http://www.igs.cnrs-mrs.fr/elnemo/start.html
• Input
  • PDB structure (file or pasted sequence)
  • Number of modes to calculate (the trivial modes 1 to 6 are excluded in this number)
  • Range of perturbation (DQMIN, DQMAX and DQSTEP)
  • Cutoff used to dentify elastic interactions
• Output
  • Animation of the vibration
  • Distance fluctations between the C-alpha atoms
  • Mean square displacement of all C-alpha atoms

References

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