Difference between revisions of "Normal mode analysis GLA"
From Bioinformatikpedia
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==WEBnm@== |
==WEBnm@== |
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| + | 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. [http://www.ncbi.nlm.nih.gov/pubmed/15762993 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. |
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| + | '''Usage''' |
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| + | * Webserver: http://apps.cbu.uib.no/webnma/home |
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| + | * Input |
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| + | ** PDB structure (ID or file) |
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| + | ** Specification of chains |
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| + | * Output |
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| + | ** Animation of vibration |
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| + | ** Deformation energy |
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| + | ** Squared atomic displacements |
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==ElNemo== |
==ElNemo== |
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Revision as of 23:42, 29 August 2011
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/>
