3D structure - Swiss Pdb Viewer David Shiuan Department of Life Science, Institute of Biotechnology...

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

a tool for viewing and manipulating protein structures and models.

tightly linked to Swiss-Model, an automated homology modeling server.

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.

Welcome to the SWISS-MODEL Protein Modelling Server    

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     <Torsten.Schwede@isb-sib.ch>   Nicolas Guex       

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@isb-sib.ch        Dr. Nicolas Guex                Dr. Manuel C. Peitsch

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

Please find enclosed your results for AAAa03uOW as an attachment.Title : lipase3D Jobid:AAAa03uOW   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.

How to visualize and analyze the Swiss-Model generated structures

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