Structure analyses: Difference between revisions
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* putative pockets in the structure | * putative pockets in the structure | ||
to be added | to be added | ||
* electrostatic surface potential | * electrostatic surface potential | ||
Use the [APBS tool in PyMOL] and visualise the surface as explained in the brief [http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html PyMOL tutorial] | Use the [APBS tool in PyMOL] and visualise the surface as explained in the brief [http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html PyMOL tutorial] | ||
* residue conservation | * residue conservation | ||
[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl Scorecons] | [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl Scorecons] | ||
* surface similarities | * surface similarities | ||
Computed atlas of surface topography of proteins [http://sts.bioengr.uic.edu/castp/calculation.php CASTp] | Computed atlas of surface topography of proteins [http://sts.bioengr.uic.edu/castp/calculation.php CASTp] | ||
--[[User:ThomasHuber|ThomasHuber]] 17:32, 25 April 2007 (EST) | --[[User:ThomasHuber|ThomasHuber]] 17:32, 25 April 2007 (EST) |
Revision as of 07:32, 25 April 2007
With the knowledge from the functional predictions from the previous section you can look closer at physical/evolutionary properties of your protein. Molecular function is dictated by the physical properties of particular amino acids in your protein and the analysis of commonalities (differences) within your protein family or with other protein structures often indicate functional similarities (differences). For example, analyse the following properties visually:
- putative pockets in the structure
to be added
- electrostatic surface potential
Use the [APBS tool in PyMOL] and visualise the surface as explained in the brief PyMOL tutorial
- residue conservation
- surface similarities
Computed atlas of surface topography of proteins CASTp
--ThomasHuber 17:32, 25 April 2007 (EST)