^{by Benjamin Drexler and Fabian Grandke}

Introduction

Methods

The following sections give a brief explanation about the methods and information about their usage.

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

Anisotropic Network Model

Anisotropic network model (ANM) is an elastic network and was introduced by Doruker et al. and Atilgan et al. in 2000<ref name=anm_doruker>Doruker P, Atilgan AR, Bahar I. "Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor.". Proteins. 2000 Aug 15;40(3):512-24. PubMed</ref><ref name=anm_atilgan>Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. "Anisotropy of fluctuation dynamics of proteins with an elastic network model.". Biophys J. 2001 Jan;80(1):505-15. PubMed</ref>. The ANM webserver is used to calculate the global modes and was published by Eyal et al. in 2006<ref name=anm_eyal>Eyal E, Yang LW, Bahar I. "Anisotropic network model: systematic evaluation and a new web interface.". Bioinformatics. 2006 Nov 1;22(21):2619-27. Epub 2006 Aug 23. PubMed</ref>. The nodes are represented by the C-alpha atoms and the calculation is based on the spring force constant γ.

Usage

Webserver: http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi
Input
- PDB structure (ID or file)
- Cutoff for interactions
- Distance weight for interactions
Output
- Animation of the vibration
- Fluctuation profiles
- Inter-residue distance fluctuations
- Deformation energies