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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
Swiss-PdbViewer
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a tool for viewing and manipulating
protein structures and models.
tightly linked to Swiss-Model, an
automated homology modeling server.
Swiss-PdbViewer
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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.
Welcome to the SWISS-MODEL
Protein Modelling Server
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Dear David Shiuan,
Title of your Request: lipase3D
Swiss-Model '(SWISS-MODEL Version 36.0003)' started
on 16-Dec-2005
Process identification is AAAa03uOW
The modelling procedure is now in progress, and its
results should be sent to you shortly.
In case of difficulties, please contact:
Torsten Schwede
Nicolas Guex
<[email protected]>
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
Dr. Nicolas Guex
Dr. Manuel C. Peitsch
[email protected]
AlignMaster output
==============
Length of target sequence: 288 residues
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Searching sequences of known 3D structures
Found 1f3rB.pdb with P(N)=6e-76
Found 1dzbB.pdb with P(N)=2e-70
Found 1dzbA.pdb with P(N)=2e-70
Found 1nqbC.pdb with P(N)=1e-66
Found 1nqbA.pdb with P(N)=1e-66
Found 1qokA.pdb with P(N)=2e-65
Found 1lmkG.pdb with P(N)=5e-64
Found 1lmkC.pdb with P(N)=5e-64
Found 1lmkE.pdb with P(N)=5e-64
Found 1lmkA.pdb with P(N)=5e-64
Found 1deeC.pdb with P(N)=8e-55
Please find enclosed your results for
AAAa03uOW as an attachment.
Title : lipase3D Jobid:AAAa03uOW Batch.1
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SWISS-MODEL project files are best viewed
using the program - DeepView, SwissPdbViewer (http://www.expasy.org/spdbv/).
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The program allows you to display and
manipulate several structures at the same
time, e.g. the model and all the superposed
templates.
How to visualize and analyze the SwissModel 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.
Hermicola (Thermomyces) lanuginaosa lipase (1DU4)
Swiss Model – Target (Ab) with 3 templates
Target (Ab) model
Target and lipase iDU4
Magic Fit – target and lipase 1DU4