As anyone else, you would like to get to results quickly. Not
only quickly, but you need to have an option for WARP speed so that you
may analyse data, rather than spend time obtaining them. So here is the manual
for SMS Warp Speed.
Also, you need to get results that should be representable, informative
and their interpretation should be intuitive.
Here we show one example of the complete description for an amino acid from
PDB file 1cho.pdb: His 57, belonging to
the E chain. We have prepared collage of images produced by STING, Ramachandran
plot, Graphical Contacts, ConSSeq
and Protein Dossier. This is the most comprehensive
data set that you can get in warp speed. Courtesy of STING Millennium Suite
ONLY.
Enjoy the cruise!
In this example, we have first initiated
STING and then asked number of question about specific amino acid: the HIS#57
in the E chain;
1) What type of internal chain contacts
this residue makes? And how many? (SMS module used: Graphical
Contacts)
___ See bottom left image {GC - Contacts Info Window}____
2) We asked to see in 3D constellation of residues
in contact with our His 57. (SMS module used: Graphical
Contacts)
___ See middle left image {STING's Graphics Window} ____
3) We were also curios to know about dihedral
angles and therefore, regularity of the structure at that specific spot.
(SMS module used: Ramachandran Plot)
___ See bottom middle image {Ramachandran Plot 1cho Window}___
4) We asked to see how much this spot was exposed to the evolutionary
pressures and what other residues also occupy this spot. (SMS module used:
ConSSeq)
___ See bottom right image {ConSSeq Applet: 1cho (Chain E) Window}___
5) Finally we asked to see all pertinent
parameters that can be calculated and shown for this specific sequence and
3D spot. (SMS module used: Protein Dossier)
___See upper right image {Protein Dossier 2 Window}___
We used only a few of SMS components in this short example, however, a number of other parameters can be calculated and shown (see for additional information below!). Also, see about extensive list of Links available through SMS that can significantly enrich volume of information you are looking for about given structure.
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