Protein sequence conservation can be a valuable tool to assess functional regions of a protein.
But sequence information can be complemented by the tridimensional structure
of the protein of interest to give new insights on the structure-function
Protein sequence conservation can be obtained from alignement engines
such as BLAST,
CLUSTAL W or GCG...
Numerous molecular modelisation programs exist to assist vizualising a 3D protein structure.
ProtSkin converts a protein sequence alignment in BLAST, CLUSTAL or MSF format
to a property file used to map the sequence conservation onto the structure of a protein using
the GRASP program or
the MOLMOL program or the PyMOL program.
A pseudo-PDB file with the sequence conservation score in place of the temperature
factor is also provided, to use with programs such as InsightII (accelrys).
You will be guided through the three following steps :
You can also use ProtSkin to map any scalar data, such as heteronuclear
NOE or chemical shift differences onto your protein structure. Prepare a
plain text file (first column : residue numbers, second column : values to
map) and go directly to step 2 to generate a GRASP property file, a MOLMOL macro or a PyMOL macro.
- Determine a sequence alignment for your protein,
- Convert this alignement,
- Use the generated file to visualize sequence conservation onto the
3D structure of your protein of interest using GRASP
or MOLMOL or PyMOL.
To acknowledge the use of ProtSkin, please cite:
Ritter B, Denisov AY, Philie J, Deprez C, Tung EC, Gehring K, McPherson PS. (2004)
Two WXXF-based motifs in NECAPs define the specificity of accessory protein binding to AP-1 and AP-2
EMBO J., 23, 3701-10
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