Difference between revisions of "Normal mode analysis GLA"
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=Methods= |
=Methods= |
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+ | Brief explanations about the methods and information about the usage are given in the following sections. |
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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. |
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''' |
'''Usage''' |
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==ElNemo== |
==ElNemo== |
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+ | 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. [http://www.ncbi.nlm.nih.gov/pubmed/15215461 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. |
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+ | '''Usage''' |
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+ | * Webserver: http://www.igs.cnrs-mrs.fr/elnemo/start.html |
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+ | * Input |
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+ | ** PDB structure (file or pasted sequence) |
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+ | ** Number of modes to calculate (the trivial modes 1 to 6 are excluded in this number) |
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+ | ** Range of perturbation (DQMIN, DQMAX and DQSTEP) |
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+ | ** Cutoff used to dentify elastic interactions |
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+ | * Output |
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+ | ** Animation of the vibration |
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+ | ** Distance fluctations between the C-alpha atoms |
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+ | ** Mean square displacement of all C-alpha atoms |
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==Anisotropic Network Model== |
==Anisotropic Network Model== |
Revision as of 00:17, 31 August 2011
by Benjamin Drexler and Fabian Grandke
Introduction
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
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/>