3D structure -Swiss Pdb Viewer

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3D structure -Swiss Pdb Viewer

• David Shiuan
• Department of Life Science,
• Institute of Biotechnology and
  Interdisciplinary Program of Bioinformatics
• National Dong Hwa University

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Swiss-PdbViewer

• a tool for viewing and manipulating protein
  structures and models.
• tightly linked to Swiss-Model, an automated
  homology modeling server.

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Swiss-PdbViewer

• provides a user friendly interface allowing to
  analyze several proteins at the same time. The
  proteins can be superimposed in order to deduce
  structural alignments and compare their active
  sites or any other relevant parts.
• Amino acid mutations, H-bonds, angles and
  distances between atoms are easy to obtain thanks
  to the intuitive graphic and menu interface.

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Welcome to the SWISS-MODEL Protein Modelling
Server    

• Dear David Shiuan,Title of your Request
  lipase3DSwiss-Model '(SWISS-MODEL Version
  36.0003)' started on 16-Dec-2005Process
  identification is AAAa03uOWThe modelling
  procedure is now in progress, and its results
  should be sent to you shortly.In case of
  difficulties, please contact   Torsten
  Schwede     ltTorsten.Schwede_at_isb-sib.chgt  
  Nicolas Guex       

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News from SWISS-MODEL  - New Server Hardware 
- DeepView - SwissPDB-Viewer   - ExPDB template
database   Good luck with your projects.The
SWISS-MODEL Team         Dr. Torsten
Schwede     Torsten.Schwede_at_isb-sib.ch       
Dr. Nicolas Guex                Dr. Manuel C.
Peitsch
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AlignMaster output Length of
target sequence 288 residues

• Searching sequences of known 3D structuresFound
  1f3rB.pdb with P(N)6e-76Found 1dzbB.pdb with
  P(N)2e-70Found 1dzbA.pdb with P(N)2e-70Found
  1nqbC.pdb with P(N)1e-66Found 1nqbA.pdb with
  P(N)1e-66Found 1qokA.pdb with P(N)2e-65Found
  1lmkG.pdb with P(N)5e-64Found 1lmkC.pdb with
  P(N)5e-64Found 1lmkE.pdb with P(N)5e-64Found
  1lmkA.pdb with P(N)5e-64Found 1deeC.pdb with
  P(N)8e-55

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Please find enclosed your results for AAAa03uOW
as an attachment.Title lipase3D
JobidAAAa03uOW   Batch.1

• SWISS-MODEL project files are best viewed using
  the program - DeepView, Swiss-PdbViewer
  (http//www.expasy.org/spdbv/).
• The program allows you to display and manipulate
  several structures at the same time, e.g. the
  model and all the superposed templates.

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How to visualize and analyze the Swiss-Model
generated structures

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• The result file can be visualized by Swiss-pdb
  Viewer or RasWin (RasMol).
• Use the Control Panel to remove all of the
  templates.
• Select known 3D structures of lipase (for
  example).
• Compare the target sequence with the known lipase
  structure by magic fit of Swiss-pdb Viewer.
• Use center the molecule on one atom tool bar to
  focus on the region of binding site.
• Compare the above two structures.

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Hermicola (Thermomyces) lanuginaosa lipase (1DU4)
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Swiss Model Target (Ab) with 3 templates
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Target (Ab) model
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Target and lipase iDU4
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Magic Fit target and lipase 1DU4