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Output format



DESCRIPTION

Example of output is found below. The output is divided into the folowinng sections:
  • Query sequence: In this section the query sequence that you submitted are shown in fasta format.
  • Searching for template: The template for building the model is sought by iteratively building up a profile by aligning the query sequence to a nonredundant database of protein sequences and then searching a database of proteins with known structure (pdb) to find a suitable template for making a model.
  • Retrieving template: In this section the pdb entry name and the chain identifier are listed for the template that are used to construct the model.
  • Making profile-profile alignment: In this section the score fro the profile profile alignment (in bits) and the percentage sequence identity between query and template are shown together with the alignment in "Blast-like" format.
  • Modeling: By clicking on the link "model.pdb" you can download the coordinates in pdb format to your own computer.
  • PDB3D: If you have an java enabled browser the C-alpha trace of the model will be shown. You can rotate it by klicking on it with the left mouse button and holding it down while mooving the mouse. The right mouse button can be used to scale the model.



EXAMPLE OUTPUT


Query sequence:

>T0155
MADRIELRGLTVHGRHGVYDHERVAGQRFVIDVTVWIDLAEAANSDDLADTYDYVRLASR
AAEIVAGPPRKLIETVGAEIADHVMDDQRVHAVEVAVHKPQAPIPQTFDDVAVVIRRSRR
GGRGWVVPAGGAV

Searching for template ...

Round   0. All hits:
entry: 1DHN chain: _ score: 67 E: 5e-12
entry: 2DHN chain: _ score: 67 E: 5e-12
entry: 1B9L chain: A score: 28 E: 3.0
entry: 1B9L chain: B score: 28 E: 3.0
entry: 1B9L chain: C score: 28 E: 3.0
entry: 1B9L chain: D score: 28 E: 3.0
entry: 1B9L chain: E score: 28 E: 3.0
entry: 1B9L chain: F score: 28 E: 3.0
entry: 1B9L chain: G score: 28 E: 3.0
entry: 1B9L chain: H score: 28 E: 3.0

Round   0. Hits better than threshold: 0.050000:
entry: 1DHN chain: _ score: 67 E: 5e-12
entry: 2DHN chain: _ score: 67 E: 5e-12

Retrieving template ...

Entry: 1dhn
Chain: _

Making profile-profile alignment ...

Score:      31.0 bits
Identity:   42.6 %

Query: 1   MADRIELRGLTVHGRHGVYDHERVAGQRFVIDVTVWIDLAEAANSDDLADTYDY 54  
           M D I L+G+  +G HG    E   GQ F +DVT  +DL EA   D   DT  Y
Templ: 1   MQDTIFLKGMRFYGYHGALSAENEIGQIFKVDVTLKVDLSEAGRTDNVIDTVHY 54  

Modeling ...


File with coordinates for model in pdb format:model.pdb





Unable to view the applet? Try the older version.





PDB3D is a high speed 3D molecule rendering applet written by Scott Legrand at UCLA.

Controls:

  1. Left Mouse Button: Rotate molecule
  2. Right Mouse Button: Scale molecule (left & right)



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